All modules for which code is available
-- sprit.sprit_cli +
- sprit.sprit_calibration +
- sprit.sprit_cli
- sprit.sprit_hvsr
- sprit.sprit_jupyter_UI
- sprit.sprit_plot +
- sprit.sprit_streamlit_ui
- sprit.sprit_tkinter_ui
- sprit.sprit_utils
- calculate_depth() (in module sprit) + + +
- calibrate() (in module sprit) + +
- catch_errors() (in module sprit)
@@ -146,6 +160,8 @@
C
- (in module sprit.sprit_utils) +
- check_if_default() (in module sprit.sprit_streamlit_ui) +
- check_instance() (in module sprit.sprit_hvsr)
- check_mark() (in module sprit)
@@ -160,14 +176,14 @@
C
- (in module sprit.sprit_hvsr) + +
- check_xvalues() (in module sprit)
-
@@ -451,6 +467,8 @@
- sprit + +
- sprit.sprit_calibration
- sprit.sprit_cli @@ -459,6 +477,8 @@
- sprit.sprit_jupyter_UI
- sprit.sprit_plot + +
- sprit.sprit_streamlit_ui
- sprit.sprit_tkinter_ui @@ -472,6 +492,12 @@
- (in module sprit.sprit_hvsr)
M
M
O
@@ -513,14 +539,26 @@+ P
- - plot_hvsr() (in module sprit) +
- plot_cross_section() (in module sprit) +
- plot_depth_curve() (in module sprit) + +
- plot_hvsr() (in module sprit) + +
- plot_outlier_curves() (in module sprit)
-
@@ -540,6 +578,8 @@
P
- plot_stream() (in module sprit.sprit_hvsr) + +
- power_law() (in module sprit.sprit_calibration)
- ppsds (sprit.HVSRData property)
@@ -553,6 +593,8 @@
P
- (sprit.sprit_hvsr.HVSRData property) +
- print_param() (in module sprit.sprit_streamlit_ui) +
- process_data() (in module sprit.sprit_plot)
- process_hvsr() (in module sprit)
@@ -619,11 +661,20 @@
R
S
-
+
- setup_session_state() (in module sprit.sprit_streamlit_ui) +
-
sprit
- module + +
+ -
+ sprit.sprit_calibration
+
+
-
+
- module
-
@@ -654,6 +705,13 @@
S
- module + +
+ -
+ sprit.sprit_streamlit_ui
+
+
-
+
- module
-
@@ -679,6 +737,8 @@
T
+-
@@ -691,6 +751,26 @@
T
U
+
+ ++ + W
+
++ + X
-
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index b3ae76b..587a7eb 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -4,7 +4,7 @@
-
assert_check()batch_data_read()calculate_azimuth()
+calculate_depth()
+calibrate()catch_errors()check_gui_requirements()check_mark()
@@ -131,6 +133,8 @@
make_it_classy()parse_plot_string()plot_azimuth()
+plot_cross_section()
+plot_depth_curve()plot_hvsr()plot_outlier_curves()plot_preview()
@@ -142,8 +146,15 @@
remove_outlier_curves()run()time_it()
+update_elevation()x_mark()- Submodules
-
+
- sprit.sprit_calibration module +
- sprit.sprit_cli module
get_param_docstring()main()
@@ -178,6 +189,7 @@
remove_outlier_curves()run()test_function()
+update_elevation()
- sprit.sprit_jupyter_UI module
-
@@ -196,6 +208,8 @@
parse_hv_plot_list()parse_plot_string()parse_spec_plot_list()
+plot_cross_section()
+plot_depth_curve()plot_outlier_curves()plot_preview()plot_results()
@@ -203,7 +217,16 @@
read_data()
- - sprit.sprit_streamlit_ui module +
- sprit.sprit_streamlit_ui module +
- sprit.sprit_tkinter_ui module
SPRIT_Appcatch_errors()
@@ -286,6 +309,7 @@
remove_outlier_curves()run()test_function()
+update_elevation()
- sprit.sprit_utils module
-
diff --git a/docs/_build/html/objects.inv b/docs/_build/html/objects.inv
index 78bd2db..16d8e11 100644
Binary files a/docs/_build/html/objects.inv and b/docs/_build/html/objects.inv differ
diff --git a/docs/_build/html/py-modindex.html b/docs/_build/html/py-modindex.html
index 0dbc6dd..dd83ef8 100644
--- a/docs/_build/html/py-modindex.html
+++ b/docs/_build/html/py-modindex.html
@@ -3,7 +3,7 @@
-
Python Module Index — sprit 2.0 documentation +Python Module Index — sprit 2.1-dev documentation @@ -12,7 +12,7 @@ - + @@ -89,6 +89,11 @@Python Module Index
sprit
<no title> — sprit 2.0 documentation +<no title> — sprit 2.1-dev documentation @@ -13,7 +13,7 @@ - + @@ -106,6 +106,8 @@+ + + sprit.sprit_calibration+ @@ -109,6 +114,11 @@ Python Module Index
sprit.sprit_plot+ + + sprit.sprit_streamlit_ui+ diff --git a/docs/_build/html/search.html b/docs/_build/html/search.html index 021830e..a03eb7f 100644 --- a/docs/_build/html/search.html +++ b/docs/_build/html/search.html @@ -3,7 +3,7 @@ - +Search — sprit 2.0 documentation +Search — sprit 2.1-dev documentation @@ -13,7 +13,7 @@ - + diff --git a/docs/_build/html/searchindex.js b/docs/_build/html/searchindex.js index 15b8b2b..3dc5f7c 100644 --- a/docs/_build/html/searchindex.js +++ b/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Contents:": [[0, null]], "Submodules": [[1, "submodules"]], "sprit package": [[1, null]], "sprit.sprit_cli module": [[2, null]], "sprit.sprit_hvsr module": [[3, null]], "sprit.sprit_jupyter_UI module": [[4, null]], "sprit.sprit_plot module": [[5, null]], "sprit.sprit_streamlit_ui module": [[6, null]], "sprit.sprit_tkinter_ui module": [[7, null]], "sprit.sprit_utils module": [[8, null]]}, "docnames": ["index", "sprit", "sprit.sprit_cli", "sprit.sprit_hvsr", "sprit.sprit_jupyter_UI", "sprit.sprit_plot", "sprit.sprit_streamlit_ui", "sprit.sprit_tkinter_ui", "sprit.sprit_utils"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["index.rst", "sprit.rst", "sprit.sprit_cli.rst", "sprit.sprit_hvsr.rst", "sprit.sprit_jupyter_UI.rst", "sprit.sprit_plot.rst", "sprit.sprit_streamlit_ui.rst", "sprit.sprit_tkinter_ui.rst", "sprit.sprit_utils.rst"], "indexentries": {"assert_check() (in module sprit)": [[1, "sprit.assert_check", false]], "assert_check() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.assert_check", false]], "batch (sprit.hvsrdata property)": [[1, "sprit.HVSRData.batch", false]], "batch (sprit.sprit_hvsr.hvsrdata property)": [[3, "sprit.sprit_hvsr.HVSRData.batch", false]], "batch_data_read() (in module sprit)": [[1, "sprit.batch_data_read", false]], "batch_data_read() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.batch_data_read", false]], "calculate_azimuth() (in module sprit)": [[1, "sprit.calculate_azimuth", false]], "calculate_azimuth() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.calculate_azimuth", false]], "catch_errors() (in module sprit)": [[1, "sprit.catch_errors", false]], "catch_errors() (in module sprit.sprit_tkinter_ui)": [[7, "sprit.sprit_tkinter_ui.catch_errors", false]], "check_gui_requirements() (in module sprit)": [[1, "sprit.check_gui_requirements", false]], "check_gui_requirements() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_gui_requirements", false]], "check_instance() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.check_instance", false]], "check_mark() (in module sprit)": [[1, "sprit.check_mark", false]], "check_mark() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_mark", false]], "check_peaks() (in module sprit)": [[1, "sprit.check_peaks", false]], "check_peaks() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.check_peaks", false]], "check_tsteps() (in module sprit)": [[1, "sprit.check_tsteps", false]], "check_tsteps() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_tsteps", false]], "check_xvalues() (in module sprit)": [[1, "sprit.check_xvalues", false]], "check_xvalues() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_xvalues", false]], "checkifpath() (in module sprit)": [[1, "sprit.checkifpath", false]], "checkifpath() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.checkifpath", false]], "copy() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.copy", false]], "copy() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.copy", false]], "copy() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.copy", false]], "copy() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.copy", false]], "create_jupyter_ui() (in module sprit)": [[1, "sprit.create_jupyter_ui", false]], "create_jupyter_ui() (in module sprit.sprit_jupyter_ui)": [[4, "sprit.sprit_jupyter_UI.create_jupyter_ui", false]], "create_menubar() (sprit.sprit_tkinter_ui.sprit_app method)": [[7, "sprit.sprit_tkinter_ui.SPRIT_App.create_menubar", false]], "create_tabs() (sprit.sprit_tkinter_ui.sprit_app method)": [[7, "sprit.sprit_tkinter_ui.SPRIT_App.create_tabs", false]], "datastream (sprit.hvsrdata property)": [[1, "sprit.HVSRData.datastream", false]], "datastream (sprit.sprit_hvsr.hvsrdata property)": [[3, "sprit.sprit_hvsr.HVSRData.datastream", false]], "export() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.export", false]], "export() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.export", false]], "export() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.export", false]], "export() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.export", false]], "export_data() (in module sprit)": [[1, "sprit.export_data", false]], "export_data() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.export_data", false]], "export_report() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.export_report", false]], "export_settings() (in module sprit)": [[1, "sprit.export_settings", false]], "export_settings() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.export_settings", false]], "export_settings() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.export_settings", false]], "export_settings() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.export_settings", false]], "export_settings() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.export_settings", false]], "export_settings() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.export_settings", false]], "fetch_data() (in module sprit)": [[1, "sprit.fetch_data", false]], "fetch_data() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.fetch_data", false]], "format_time() (in module sprit)": [[1, "sprit.format_time", false]], "format_time() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.format_time", false]], "generate_ppsds() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.generate_ppsds", false]], "generate_psds() (in module sprit)": [[1, "sprit.generate_psds", false]], "generate_psds() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.generate_psds", false]], "get_char() (in module sprit)": [[1, "sprit.get_char", false]], "get_char() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.get_char", false]], "get_check_peaks_kwargs() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.get_check_peaks_kwargs", false]], "get_default() (in module sprit.sprit_jupyter_ui)": [[4, "sprit.sprit_jupyter_UI.get_default", false]], "get_default_args() (in module sprit)": [[1, "sprit.get_default_args", false]], "get_default_args() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.get_default_args", false]], "get_generate_ppsd_kwargs() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.get_generate_ppsd_kwargs", false]], "get_get_report_kwargs() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.get_get_report_kwargs", false]], "get_metadata() (in module sprit)": [[1, "sprit.get_metadata", false]], "get_metadata() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.get_metadata", false]], "get_param_docstring() (in module sprit.sprit_cli)": [[2, "sprit.sprit_cli.get_param_docstring", false]], "get_process_hvsr_kwargs() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.get_process_hvsr_kwargs", false]], "get_remove_noise_kwargs() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.get_remove_noise_kwargs", false]], "get_remove_outlier_curve_kwargs() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.get_remove_outlier_curve_kwargs", false]], "get_report() (in module sprit)": [[1, "sprit.get_report", false]], "get_report() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.get_report", false]], "get_report() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.get_report", false]], "get_report() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.get_report", false]], "get_report() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.get_report", false]], "get_report() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.get_report", false]], "gui() (in module sprit)": [[1, "sprit.gui", false]], "gui() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.gui", false]], "gui_test() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.gui_test", false]], "has_required_channels() (in module sprit)": [[1, "sprit.has_required_channels", false]], "has_required_channels() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.has_required_channels", false]], "hvsrbatch (class in sprit)": [[1, "sprit.HVSRBatch", false]], "hvsrbatch (class in sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.HVSRBatch", false]], "hvsrdata (class in sprit)": [[1, "sprit.HVSRData", false]], "hvsrdata (class in sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.HVSRData", false]], "import_data() (in module sprit)": [[1, "sprit.import_data", false]], "import_data() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.import_data", false]], "import_settings() (in module sprit)": [[1, "sprit.import_settings", false]], "import_settings() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.import_settings", false]], "input_params() (in module sprit)": [[1, "sprit.input_params", false]], "input_params() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.input_params", false]], "items() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.items", false]], "items() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.items", false]], "items() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.items", false]], "items() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.items", false]], "keys() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.keys", false]], "keys() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.keys", false]], "keys() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.keys", false]], "keys() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.keys", false]], "log_errormsg() (sprit.sprit_tkinter_ui.sprit_app method)": [[7, "sprit.sprit_tkinter_ui.SPRIT_App.log_errorMsg", false]], "main() (in module sprit.sprit_cli)": [[2, "sprit.sprit_cli.main", false]], "make_it_classy() (in module sprit)": [[1, "sprit.make_it_classy", false]], "make_it_classy() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.make_it_classy", false]], "manual_label_update() (sprit.sprit_tkinter_ui.sprit_app method)": [[7, "sprit.sprit_tkinter_ui.SPRIT_App.manual_label_update", false]], "module": [[1, "module-sprit", false], [2, "module-sprit.sprit_cli", false], [3, "module-sprit.sprit_hvsr", false], [4, "module-sprit.sprit_jupyter_UI", false], [5, "module-sprit.sprit_plot", false], [7, "module-sprit.sprit_tkinter_ui", false], [8, "module-sprit.sprit_utils", false]], "on_closing() (in module sprit.sprit_tkinter_ui)": [[7, "sprit.sprit_tkinter_ui.on_closing", false]], "params (sprit.hvsrdata property)": [[1, "sprit.HVSRData.params", false]], "params (sprit.sprit_hvsr.hvsrdata property)": [[3, "sprit.sprit_hvsr.HVSRData.params", false]], "parse_comp_plot_list() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.parse_comp_plot_list", false]], "parse_hv_plot_list() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.parse_hv_plot_list", false]], "parse_plot_string() (in module sprit)": [[1, "sprit.parse_plot_string", false]], "parse_plot_string() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.parse_plot_string", false]], "parse_spec_plot_list() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.parse_spec_plot_list", false]], "plot() (sprit.hvsrbatch method)": [[1, "sprit.HVSRBatch.plot", false]], "plot() (sprit.hvsrdata method)": [[1, "sprit.HVSRData.plot", false]], "plot() (sprit.sprit_hvsr.hvsrbatch method)": [[3, "sprit.sprit_hvsr.HVSRBatch.plot", false]], "plot() (sprit.sprit_hvsr.hvsrdata method)": [[3, "sprit.sprit_hvsr.HVSRData.plot", false]], "plot_azimuth() (in module sprit)": [[1, "sprit.plot_azimuth", false]], "plot_azimuth() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.plot_azimuth", false]], "plot_hvsr() (in module sprit)": [[1, "sprit.plot_hvsr", false]], "plot_hvsr() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.plot_hvsr", false]], "plot_outlier_curves() (in module sprit)": [[1, "sprit.plot_outlier_curves", false]], "plot_outlier_curves() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.plot_outlier_curves", false]], "plot_preview() (in module sprit)": [[1, "sprit.plot_preview", false]], "plot_preview() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.plot_preview", false]], "plot_results() (in module sprit)": [[1, "sprit.plot_results", false]], "plot_results() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.plot_results", false]], "plot_stream() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.plot_stream", false]], "ppsds (sprit.hvsrdata property)": [[1, "sprit.HVSRData.ppsds", false]], "ppsds (sprit.sprit_hvsr.hvsrdata property)": [[3, "sprit.sprit_hvsr.HVSRData.ppsds", false]], "ppsds_obspy (sprit.hvsrdata property)": [[1, "sprit.HVSRData.ppsds_obspy", false]], "ppsds_obspy (sprit.sprit_hvsr.hvsrdata property)": [[3, "sprit.sprit_hvsr.HVSRData.ppsds_obspy", false]], "process_data() (in module sprit.sprit_plot)": [[5, "sprit.sprit_plot.process_data", false]], "process_hvsr() (in module sprit)": [[1, "sprit.process_hvsr", false]], "process_hvsr() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.process_hvsr", false]], "read_data() (in module 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4, "you": [1, 3, 4], "your": [1, 3, 4], "yyyi": [1, 4], "z": [1, 4, 6], "zero": [1, 4], "zerophas": [1, 4]}, "titles": ["<no title>", "sprit package", "sprit.sprit_calibration module", "sprit.sprit_cli module", "sprit.sprit_hvsr module", "sprit.sprit_jupyter_UI module", "sprit.sprit_plot module", "sprit.sprit_streamlit_ui module", "sprit.sprit_tkinter_ui module", "sprit.sprit_utils module"], "titleterms": {"content": 0, "modul": [2, 3, 4, 5, 6, 7, 8, 9], "packag": 1, "sprit": [1, 2, 3, 4, 5, 6, 7, 8, 9], "sprit_calibr": 2, "sprit_cli": 3, "sprit_hvsr": 4, "sprit_jupyter_ui": 5, "sprit_plot": 6, "sprit_streamlit_ui": 7, "sprit_tkinter_ui": 8, "sprit_util": 9, "submodul": 1}}) \ No newline at end of file diff --git a/docs/_build/html/sprit.html b/docs/_build/html/sprit.html index dfafa3f..094b0e2 100644 --- a/docs/_build/html/sprit.html +++ b/docs/_build/html/sprit.html @@ -4,7 +4,7 @@ -sprit package — sprit 2.0 documentation +sprit package — sprit 2.1-dev documentation @@ -13,13 +13,13 @@ - + - + @@ -75,6 +75,8 @@assert_check()batch_data_read()calculate_azimuth()calculate_depth()calibrate()catch_errors()check_gui_requirements()check_mark()make_it_classy()parse_plot_string()plot_azimuth()plot_cross_section()plot_depth_curve()plot_hvsr()plot_outlier_curves()plot_preview()remove_outlier_curves()run()time_it()update_elevation()x_mark()- Submodules
-
+
- sprit.sprit_calibration module
- sprit.sprit_cli module
- sprit.sprit_hvsr module
- sprit.sprit_jupyter_UI module @@ -668,6 +674,55 @@ +
- +sprit.calculate_depth(freq_input, depth_model='ISGS_All', freq_col='Peak', calculate_depth_in_feet=False, calculate_elevation=True, show_depth_curve=True, surface_elevation_data='Elevation', bedrock_elevation_column='BedrockElevation', depth_column='BedrockDepth', verbose=False, export_path=None, swave_velocity=563.0, decimal_places=3, depth_model_in_latex=False, fig=None, ax=None, **kwargs)[source]¶ +
Calculate depth(s) based on a frequency input (usually HVSRData or HVSRBatch oject) and a frequency-depth depth_model (usually a power law relationship).
+-
+
- Parameters: +
-
+
- freq_inputHVSRData, HVSRBatch, float, or filepath, optional
Input with frequency information, by default {sprit_hvsr.HVSRData, sprit_hvsr.HVSRBatch, float, os.PathLike}
+
+- depth_modelstr, tuple, list, or dict, optional
Model describing a relationship between frequency and depth, by default “ISGS_All”
+
+- calculate_depth_in_feetbool, optional
Whether to calculate depth in feet (in addition to meters, which is done by default)
+
+- freq_colstr, optional
Name of the column containing the frequency information of the peak, by default “Peak” (per HVSRData.Table_Report output)
+
+- calculate_elevationbool, optional
Whether or not to calculate elevation, by default True
+
+- surface_elevation_datastr or numeric, optional
The name of the column or a manually specified numeric value to use for the surface elevation value, by default “Elevation”
+
+- bedrock_elevation_columnstr, optional
The name of the column in the TableReport for the bedrock elevation of the point. +This can be either the name of a column in a table (i.e., Table_Report) or a numeric value, by default “BedrockElevation”
+
+- depth_columnstr, optional
_description_, by default “BedrockDepth”
+
+- verbosebool, optional
Whether or not to print information about the processing to the terminal, by default False
+
+- export_path_type_, optional
_description_, by default None
+
+- swave_velocityfloat, optional
Shear wave velocity to use for depth calculations in meters/second, +if using the quarter wavelength shear wave velocity method, by default 563.0
+
+- decimal_placesint, optional
Number of decimal places to round depth results, by default 3
+
+
+- Returns: +
-
+
- HVSRBatch or list if those are input; otherwise, HVSRData object
The returns are the same type as freq_input, except filepath which returns pandas.DataFrame
+
+
+
- +sprit.calibrate(calib_filepath, calib_type='power', outlier_radius=None, bedrock_type=None, peak_freq_col='PeakFrequency', bed_depth_col='Bedrock_Depth', **kwargs)[source]¶ +
- sprit.catch_errors(func)[source]¶ @@ -1061,7 +1116,7 @@
- -sprit.import_data(import_filepath, data_format='pickle')[source]¶ +sprit.import_data(import_filepath, data_format='pickle', show_data=False)[source]¶
Function to import .hvsr (or other extension) data exported using export_data() function
- Parameters: @@ -1087,7 +1142,7 @@
- -sprit.input_params(input_data, site='HVSR Site', project=None, network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2024-11-09', starttime=UTCDateTime(2024, 11, 9, 0, 0), endtime=UTCDateTime(2024, 11, 9, 23, 59, 59, 999999), tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs=None, output_crs=None, elev_unit='meters', depth=0, instrument='Raspberry Shake', metapath=None, hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], processing_parameters={}, verbose=False)[source]¶ +sprit.input_params(input_data, site='HVSR Site', project=None, network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2025-01-15', starttime=UTCDateTime(2025, 1, 15, 0, 0), endtime=UTCDateTime(2025, 1, 15, 23, 59, 59, 999999), tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs=None, output_crs=None, elev_unit='meters', depth=0, instrument='Raspberry Shake', metapath=None, hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], processing_parameters={}, verbose=False)[source]¶
Function for designating input parameters for reading in and processing data
- Parameters: @@ -1201,6 +1256,16 @@
- +sprit.plot_cross_section(hvsr_data, title=None, fig=None, ax=None, use_elevation=True, show_feet=False, primary_unit='m', show_curves=True, annotate_curves=False, curve_alignment='peak', grid_size='auto', orientation='WE', interpolation_type='cloughtocher', surface_elevations=None, show_peak_points=True, smooth_bedrock_surface=False, depth_limit=150, minimum_elevation=None, show_bedrock_surface=True, return_data_batch=True, show_cross_section=True, verbose=False, **kwargs)[source]¶ +
- +sprit.plot_depth_curve(hvsr_results, use_elevation=True, show_feet=False, normalize_curve=True, depth_limit=250, max_elev=None, min_elev=None, annotate=True, depth_plot_export_path=None, fig=None, ax=None, show_depth_curve=True)[source]¶ +
- sprit.plot_hvsr(hvsr_data, plot_type='HVSR p ann COMP+ p ann SPEC p ann', azimuth='HV', use_subplots=True, fig=None, ax=None, return_fig=False, plot_engine='matplotlib', save_dir=None, save_suffix='', show_legend=False, show_plot=True, close_figs=False, clear_fig=True, **kwargs)[source]¶ @@ -1580,11 +1645,11 @@
-
+
-
+
- channels: any, default = [‘EHZ’, ‘EHN’, ‘EHE’]
See API documentation at link above or at help(input_params) for specifics.
-- acq_date: any, default = ‘2024-11-09’
See API documentation at link above or at help(sprit.input_params) for specifics.
+- acq_date: any, default = ‘2025-01-15’
See API documentation at link above or at help(sprit.input_params) for specifics.
-- starttime: any, default = 2024-11-09T00:00:00.000000Z
See API documentation at link above or at help(input_params) for specifics.
+- starttime: any, default = 2025-01-15T00:00:00.000000Z
See API documentation at link above or at help(input_params) for specifics.
-- endtime: any, default = 2024-11-09T23:59:59.999999Z
See API documentation at link above or at help(input_params) for specifics.
+- endtime: any, default = 2025-01-15T23:59:59.999999Z
See API documentation at link above or at help(input_params) for specifics.
- tzone: any, default = ‘UTC’
See API documentation at link above or at help(sprit.input_params) for specifics.
@@ -1865,6 +1930,33 @@
Computes elapsed time since the last call.
- +sprit.update_elevation(hvsr_data, updated_surface_elevation, updated_elevation_unit)[source]¶ +
Function to quickly update all attributes associated with elevation of an HVSRData object
+-
+
- Parameters: +
-
+
- hvsr_dataHVSRData or HVSRBatch
HVSRData or HVSRBatch object containing attributes related to elevation. +If HVSRBatch, updated_surface_elevation should be list or tuple and +updated_elevation_unit may either be str or list/tuple of strings.
+
+- updated_surface_elevationnumbers.Number
Number (float or int) with the updated elevation. +Meters is the preferred unit. If feet are used instead, it will be converted to meters.
+
+- updated_elevation_unitstr
Unit used for updated_surface_elevation. If ‘feet’, it will be converted to meters.
+
+
+- Returns: +
-
+
- HVSRData
HVSRData object with all attributes related to elevation updated
+
+
+
- sprit.x_mark(incolor=False, inTerminal=False)[source]¶ @@ -1876,6 +1968,12 @@
- sprit.sprit_calibration module +
- sprit.sprit_cli module
get_param_docstring()main()
@@ -1935,6 +2033,7 @@
Submodules
remove_outlier_curves() run()test_function()
+update_elevation()- sprit.sprit_jupyter_UI module
-
@@ -1953,6 +2052,8 @@
Submodules
parse_hv_plot_list() parse_plot_string()parse_spec_plot_list()
+plot_cross_section()
+plot_depth_curve()plot_outlier_curves()plot_preview()plot_results()
@@ -1960,7 +2061,16 @@ - sprit.sprit_streamlit_ui module +
- sprit.sprit_streamlit_ui module +
- sprit.sprit_tkinter_ui module
SPRIT_AppSPRIT_App.create_menubar()
@@ -2001,7 +2111,7 @@
Submodules Previous - Next + Next
- +sprit.sprit_calibration.calculate_depth(freq_input, depth_model='ISGS_All', freq_col='Peak', calculate_depth_in_feet=False, calculate_elevation=True, show_depth_curve=True, surface_elevation_data='Elevation', bedrock_elevation_column='BedrockElevation', depth_column='BedrockDepth', verbose=False, export_path=None, swave_velocity=563.0, decimal_places=3, depth_model_in_latex=False, fig=None, ax=None, **kwargs)[source]¶ +
Calculate depth(s) based on a frequency input (usually HVSRData or HVSRBatch oject) and a frequency-depth depth_model (usually a power law relationship).
+-
+
- Parameters: +
-
+
- freq_inputHVSRData, HVSRBatch, float, or filepath, optional
Input with frequency information, by default {sprit_hvsr.HVSRData, sprit_hvsr.HVSRBatch, float, os.PathLike}
+
+- depth_modelstr, tuple, list, or dict, optional
Model describing a relationship between frequency and depth, by default “ISGS_All”
+
+- calculate_depth_in_feetbool, optional
Whether to calculate depth in feet (in addition to meters, which is done by default)
+
+- freq_colstr, optional
Name of the column containing the frequency information of the peak, by default “Peak” (per HVSRData.Table_Report output)
+
+- calculate_elevationbool, optional
Whether or not to calculate elevation, by default True
+
+- surface_elevation_datastr or numeric, optional
The name of the column or a manually specified numeric value to use for the surface elevation value, by default “Elevation”
+
+- bedrock_elevation_columnstr, optional
The name of the column in the TableReport for the bedrock elevation of the point. +This can be either the name of a column in a table (i.e., Table_Report) or a numeric value, by default “BedrockElevation”
+
+- depth_columnstr, optional
_description_, by default “BedrockDepth”
+
+- verbosebool, optional
Whether or not to print information about the processing to the terminal, by default False
+
+- export_path_type_, optional
_description_, by default None
+
+- swave_velocityfloat, optional
Shear wave velocity to use for depth calculations in meters/second, +if using the quarter wavelength shear wave velocity method, by default 563.0
+
+- decimal_placesint, optional
Number of decimal places to round depth results, by default 3
+
+
+- Returns: +
-
+
- HVSRBatch or list if those are input; otherwise, HVSRData object
The returns are the same type as freq_input, except filepath which returns pandas.DataFrame
+
+
+
assert_check()batch_data_read()calculate_azimuth()
+calculate_depth()
+calibrate()catch_errors()check_gui_requirements()check_mark()
@@ -75,6 +77,8 @@
make_it_classy()parse_plot_string()plot_azimuth()
+plot_cross_section()
+plot_depth_curve()plot_hvsr()plot_outlier_curves()plot_preview()
@@ -86,8 +90,10 @@
remove_outlier_curves()run()time_it()
+update_elevation()x_mark()- Submodules
-
+
- sprit.sprit_calibration module
- sprit.sprit_cli module
get_param_docstring()main()
@@ -154,7 +160,7 @@
-
+
-
+
-
+
Submodules¶
-
+
Submodules
read_data()-
diff --git a/docs/_build/html/sprit.sprit_calibration.html b/docs/_build/html/sprit.sprit_calibration.html new file mode 100644 index 0000000..d28e037 --- /dev/null +++ b/docs/_build/html/sprit.sprit_calibration.html @@ -0,0 +1,233 @@ + + + + + + +sprit.sprit_calibration module — sprit 2.1-dev documentation + + + + + + + + + + + + + + + + + ++ + ++ + + + \ No newline at end of file diff --git a/docs/_build/html/sprit.sprit_cli.html b/docs/_build/html/sprit.sprit_cli.html index 7ec3ca7..d01ea5b 100644 --- a/docs/_build/html/sprit.sprit_cli.html +++ b/docs/_build/html/sprit.sprit_cli.html @@ -4,7 +4,7 @@ -+ + ++++ ++++ ++ +++ + + +sprit.sprit_calibration module¶
+This module will be used for calibration of the ambient HVSR data acquired near wells +to derive a relation between the resonant frequency and the depth to bedrock beneath the subsurface.
+-
+
sprit.sprit_cli module — sprit 2.0 documentation +sprit.sprit_cli module — sprit 2.1-dev documentation @@ -13,14 +13,14 @@ - + - + @@ -50,6 +50,8 @@- - check_xvalues() (in module sprit)
-
@@ -451,6 +467,8 @@
- sprit + +
- sprit.sprit_calibration
- sprit.sprit_cli @@ -459,6 +477,8 @@
- sprit.sprit_jupyter_UI
- sprit.sprit_plot + +
- sprit.sprit_streamlit_ui
- sprit.sprit_tkinter_ui @@ -472,6 +492,12 @@
- (in module sprit.sprit_hvsr)
M
M
O
@@ -513,14 +539,26 @@+ P
- - plot_hvsr() (in module sprit) +
- plot_cross_section() (in module sprit) +
- plot_depth_curve() (in module sprit) + +
-
+
- plot_hvsr() (in module sprit) + +
- plot_outlier_curves() (in module sprit)
-
@@ -540,6 +578,8 @@
P
- plot_stream() (in module sprit.sprit_hvsr) +
+- power_law() (in module sprit.sprit_calibration)
- ppsds (sprit.HVSRData property) @@ -553,6 +593,8 @@
P
- (sprit.sprit_hvsr.HVSRData property)
+- print_param() (in module sprit.sprit_streamlit_ui) +
- process_data() (in module sprit.sprit_plot)
- process_hvsr() (in module sprit) @@ -619,11 +661,20 @@
R
S
-
+
- setup_session_state() (in module sprit.sprit_streamlit_ui) +
-
sprit
- module + +
+ -
+ sprit.sprit_calibration
+
+
-
+
- module
-
@@ -654,6 +705,13 @@
S
- module + +
+ -
+ sprit.sprit_streamlit_ui
+
+
-
+
- module
-
@@ -679,6 +737,8 @@
T
+-
@@ -691,6 +751,26 @@
T
U
+
+ ++ + W
+
++ + X
-
diff --git a/docs/index.html b/docs/index.html
index a353db2..5bcdb49 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,7 +4,7 @@
-
assert_check()batch_data_read()calculate_azimuth()
+calculate_depth()
+calibrate()catch_errors()check_gui_requirements()check_mark()
@@ -131,6 +133,8 @@
make_it_classy()parse_plot_string()plot_azimuth()
+plot_cross_section()
+plot_depth_curve()plot_hvsr()plot_outlier_curves()plot_preview()
@@ -142,8 +146,15 @@
remove_outlier_curves()run()time_it()
+update_elevation()x_mark()- Submodules
-
+
- sprit.sprit_calibration module +
- sprit.sprit_cli module
get_param_docstring()main()
@@ -178,6 +189,7 @@
remove_outlier_curves()run()test_function()
+update_elevation()
- sprit.sprit_jupyter_UI module
-
@@ -196,6 +208,8 @@
parse_hv_plot_list()parse_plot_string()parse_spec_plot_list()
+plot_cross_section()
+plot_depth_curve()plot_outlier_curves()plot_preview()plot_results()
@@ -203,7 +217,16 @@
read_data()
- - sprit.sprit_streamlit_ui module +
- sprit.sprit_streamlit_ui module +
- sprit.sprit_tkinter_ui module
SPRIT_Appcatch_errors()
@@ -286,6 +309,7 @@
remove_outlier_curves()run()test_function()
+update_elevation()
- sprit.sprit_utils module
-
diff --git a/docs/objects.inv b/docs/objects.inv
index 78bd2db..16d8e11 100644
Binary files a/docs/objects.inv and b/docs/objects.inv differ
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index 88cc17c..8a8dc30 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -3,7 +3,7 @@
-
Python Module Index — sprit 2.0 documentation +Python Module Index — sprit 2.1-dev documentation @@ -12,7 +12,7 @@ - + @@ -89,6 +89,11 @@Python Module Index
sprit
<no title> — sprit 2.0 documentation +<no title> — sprit 2.1-dev documentation @@ -13,7 +13,7 @@ - + @@ -106,6 +106,8 @@+ + + sprit.sprit_calibration+ @@ -109,6 +114,11 @@ Python Module Index
sprit.sprit_plot+ + + sprit.sprit_streamlit_ui+ diff --git a/docs/requirements.txt b/docs/requirements.txt index 4b5db99..d681f3f 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -12,4 +12,4 @@ sphinx markdown pytest flake8 -sprit==2.0 \ No newline at end of file +sprit==2.1.dev0 \ No newline at end of file diff --git a/docs/search.html b/docs/search.html index 1f49102..721a1a0 100644 --- a/docs/search.html +++ b/docs/search.html @@ -3,7 +3,7 @@ - Search — sprit 2.0 documentation +Search — sprit 2.1-dev documentation @@ -13,7 +13,7 @@ - + diff --git a/docs/searchindex.js b/docs/searchindex.js index 15b8b2b..3dc5f7c 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Contents:": [[0, null]], "Submodules": [[1, "submodules"]], "sprit package": [[1, null]], "sprit.sprit_cli module": [[2, null]], "sprit.sprit_hvsr module": [[3, null]], "sprit.sprit_jupyter_UI module": [[4, null]], "sprit.sprit_plot module": [[5, null]], "sprit.sprit_streamlit_ui module": [[6, null]], "sprit.sprit_tkinter_ui module": [[7, null]], "sprit.sprit_utils module": [[8, null]]}, "docnames": ["index", "sprit", "sprit.sprit_cli", "sprit.sprit_hvsr", "sprit.sprit_jupyter_UI", "sprit.sprit_plot", "sprit.sprit_streamlit_ui", "sprit.sprit_tkinter_ui", "sprit.sprit_utils"], "envversion": {"sphinx": 62, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1}, "filenames": ["index.rst", "sprit.rst", "sprit.sprit_cli.rst", "sprit.sprit_hvsr.rst", "sprit.sprit_jupyter_UI.rst", "sprit.sprit_plot.rst", "sprit.sprit_streamlit_ui.rst", "sprit.sprit_tkinter_ui.rst", "sprit.sprit_utils.rst"], "indexentries": {"assert_check() (in module sprit)": [[1, "sprit.assert_check", false]], "assert_check() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.assert_check", false]], "batch (sprit.hvsrdata property)": [[1, "sprit.HVSRData.batch", false]], "batch (sprit.sprit_hvsr.hvsrdata property)": [[3, "sprit.sprit_hvsr.HVSRData.batch", false]], "batch_data_read() (in module sprit)": [[1, "sprit.batch_data_read", false]], "batch_data_read() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.batch_data_read", false]], "calculate_azimuth() (in module sprit)": [[1, "sprit.calculate_azimuth", false]], "calculate_azimuth() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.calculate_azimuth", false]], "catch_errors() (in module sprit)": [[1, "sprit.catch_errors", false]], "catch_errors() (in module sprit.sprit_tkinter_ui)": [[7, "sprit.sprit_tkinter_ui.catch_errors", false]], "check_gui_requirements() (in module sprit)": [[1, "sprit.check_gui_requirements", false]], "check_gui_requirements() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_gui_requirements", false]], "check_instance() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.check_instance", false]], "check_mark() (in module sprit)": [[1, "sprit.check_mark", false]], "check_mark() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_mark", false]], "check_peaks() (in module sprit)": [[1, "sprit.check_peaks", false]], "check_peaks() (in module sprit.sprit_hvsr)": [[3, "sprit.sprit_hvsr.check_peaks", false]], "check_tsteps() (in module sprit)": [[1, "sprit.check_tsteps", false]], "check_tsteps() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_tsteps", false]], "check_xvalues() (in module sprit)": [[1, "sprit.check_xvalues", false]], "check_xvalues() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.check_xvalues", false]], "checkifpath() (in module sprit)": [[1, "sprit.checkifpath", false]], "checkifpath() (in module sprit.sprit_utils)": [[8, "sprit.sprit_utils.checkifpath", false]], "copy() 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[1, 4], "ycoord": [1, 4], "year": [1, 4, 9], "ylim_std": 4, "you": [1, 3, 4], "your": [1, 3, 4], "yyyi": [1, 4], "z": [1, 4, 6], "zero": [1, 4], "zerophas": [1, 4]}, "titles": ["<no title>", "sprit package", "sprit.sprit_calibration module", "sprit.sprit_cli module", "sprit.sprit_hvsr module", "sprit.sprit_jupyter_UI module", "sprit.sprit_plot module", "sprit.sprit_streamlit_ui module", "sprit.sprit_tkinter_ui module", "sprit.sprit_utils module"], "titleterms": {"content": 0, "modul": [2, 3, 4, 5, 6, 7, 8, 9], "packag": 1, "sprit": [1, 2, 3, 4, 5, 6, 7, 8, 9], "sprit_calibr": 2, "sprit_cli": 3, "sprit_hvsr": 4, "sprit_jupyter_ui": 5, "sprit_plot": 6, "sprit_streamlit_ui": 7, "sprit_tkinter_ui": 8, "sprit_util": 9, "submodul": 1}}) \ No newline at end of file diff --git a/docs/sprit.html b/docs/sprit.html index edc44a6..c83b360 100644 --- a/docs/sprit.html +++ b/docs/sprit.html @@ -4,7 +4,7 @@ -sprit package — sprit 2.0 documentation +sprit package — sprit 2.1-dev documentation @@ -13,13 +13,13 @@ - + - + @@ -75,6 +75,8 @@assert_check()batch_data_read()calculate_azimuth()calculate_depth()calibrate()catch_errors()check_gui_requirements()check_mark()make_it_classy()parse_plot_string()plot_azimuth()plot_cross_section()plot_depth_curve()plot_hvsr()plot_outlier_curves()plot_preview()remove_outlier_curves()run()time_it()update_elevation()x_mark()- Submodules
-
+
- sprit.sprit_calibration module
- sprit.sprit_cli module
- sprit.sprit_hvsr module
- sprit.sprit_jupyter_UI module @@ -668,6 +674,55 @@ +
- +sprit.calculate_depth(freq_input, depth_model='ISGS_All', freq_col='Peak', calculate_depth_in_feet=False, calculate_elevation=True, show_depth_curve=True, surface_elevation_data='Elevation', bedrock_elevation_column='BedrockElevation', depth_column='BedrockDepth', verbose=False, export_path=None, swave_velocity=563.0, decimal_places=3, depth_model_in_latex=False, fig=None, ax=None, **kwargs)[source]¶ +
Calculate depth(s) based on a frequency input (usually HVSRData or HVSRBatch oject) and a frequency-depth depth_model (usually a power law relationship).
+-
+
- Parameters: +
-
+
- freq_inputHVSRData, HVSRBatch, float, or filepath, optional
Input with frequency information, by default {sprit_hvsr.HVSRData, sprit_hvsr.HVSRBatch, float, os.PathLike}
+
+- depth_modelstr, tuple, list, or dict, optional
Model describing a relationship between frequency and depth, by default “ISGS_All”
+
+- calculate_depth_in_feetbool, optional
Whether to calculate depth in feet (in addition to meters, which is done by default)
+
+- freq_colstr, optional
Name of the column containing the frequency information of the peak, by default “Peak” (per HVSRData.Table_Report output)
+
+- calculate_elevationbool, optional
Whether or not to calculate elevation, by default True
+
+- surface_elevation_datastr or numeric, optional
The name of the column or a manually specified numeric value to use for the surface elevation value, by default “Elevation”
+
+- bedrock_elevation_columnstr, optional
The name of the column in the TableReport for the bedrock elevation of the point. +This can be either the name of a column in a table (i.e., Table_Report) or a numeric value, by default “BedrockElevation”
+
+- depth_columnstr, optional
_description_, by default “BedrockDepth”
+
+- verbosebool, optional
Whether or not to print information about the processing to the terminal, by default False
+
+- export_path_type_, optional
_description_, by default None
+
+- swave_velocityfloat, optional
Shear wave velocity to use for depth calculations in meters/second, +if using the quarter wavelength shear wave velocity method, by default 563.0
+
+- decimal_placesint, optional
Number of decimal places to round depth results, by default 3
+
+
+- Returns: +
-
+
- HVSRBatch or list if those are input; otherwise, HVSRData object
The returns are the same type as freq_input, except filepath which returns pandas.DataFrame
+
+
+
- +sprit.calibrate(calib_filepath, calib_type='power', outlier_radius=None, bedrock_type=None, peak_freq_col='PeakFrequency', bed_depth_col='Bedrock_Depth', **kwargs)[source]¶ +
- sprit.catch_errors(func)[source]¶ @@ -1061,7 +1116,7 @@
- -sprit.import_data(import_filepath, data_format='pickle')[source]¶ +sprit.import_data(import_filepath, data_format='pickle', show_data=False)[source]¶
Function to import .hvsr (or other extension) data exported using export_data() function
- Parameters: @@ -1087,7 +1142,7 @@
- -sprit.input_params(input_data, site='HVSR Site', project=None, network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2024-11-09', starttime=UTCDateTime(2024, 11, 9, 0, 0), endtime=UTCDateTime(2024, 11, 9, 23, 59, 59, 999999), tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs=None, output_crs=None, elev_unit='meters', depth=0, instrument='Raspberry Shake', metapath=None, hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], processing_parameters={}, verbose=False)[source]¶ +sprit.input_params(input_data, site='HVSR Site', project=None, network='AM', station='RAC84', loc='00', channels=['EHZ', 'EHN', 'EHE'], acq_date='2025-01-15', starttime=UTCDateTime(2025, 1, 15, 0, 0), endtime=UTCDateTime(2025, 1, 15, 23, 59, 59, 999999), tzone='UTC', xcoord=-88.2290526, ycoord=40.1012122, elevation=755, input_crs=None, output_crs=None, elev_unit='meters', depth=0, instrument='Raspberry Shake', metapath=None, hvsr_band=[0.4, 40], peak_freq_range=[0.4, 40], processing_parameters={}, verbose=False)[source]¶
Function for designating input parameters for reading in and processing data
- Parameters: @@ -1201,6 +1256,16 @@
- +sprit.plot_cross_section(hvsr_data, title=None, fig=None, ax=None, use_elevation=True, show_feet=False, primary_unit='m', show_curves=True, annotate_curves=False, curve_alignment='peak', grid_size='auto', orientation='WE', interpolation_type='cloughtocher', surface_elevations=None, show_peak_points=True, smooth_bedrock_surface=False, depth_limit=150, minimum_elevation=None, show_bedrock_surface=True, return_data_batch=True, show_cross_section=True, verbose=False, **kwargs)[source]¶ +
- +sprit.plot_depth_curve(hvsr_results, use_elevation=True, show_feet=False, normalize_curve=True, depth_limit=250, max_elev=None, min_elev=None, annotate=True, depth_plot_export_path=None, fig=None, ax=None, show_depth_curve=True)[source]¶ +
- sprit.plot_hvsr(hvsr_data, plot_type='HVSR p ann COMP+ p ann SPEC p ann', azimuth='HV', use_subplots=True, fig=None, ax=None, return_fig=False, plot_engine='matplotlib', save_dir=None, save_suffix='', show_legend=False, show_plot=True, close_figs=False, clear_fig=True, **kwargs)[source]¶ @@ -1580,11 +1645,11 @@
-
+
-
+
- channels: any, default = [‘EHZ’, ‘EHN’, ‘EHE’]
See API documentation at link above or at help(input_params) for specifics.
-- acq_date: any, default = ‘2024-11-09’
See API documentation at link above or at help(sprit.input_params) for specifics.
+- acq_date: any, default = ‘2025-01-15’
See API documentation at link above or at help(sprit.input_params) for specifics.
-- starttime: any, default = 2024-11-09T00:00:00.000000Z
See API documentation at link above or at help(input_params) for specifics.
+- starttime: any, default = 2025-01-15T00:00:00.000000Z
See API documentation at link above or at help(input_params) for specifics.
-- endtime: any, default = 2024-11-09T23:59:59.999999Z
See API documentation at link above or at help(input_params) for specifics.
+- endtime: any, default = 2025-01-15T23:59:59.999999Z
See API documentation at link above or at help(input_params) for specifics.
- tzone: any, default = ‘UTC’
See API documentation at link above or at help(sprit.input_params) for specifics.
@@ -1865,6 +1930,33 @@
Computes elapsed time since the last call.
- +sprit.update_elevation(hvsr_data, updated_surface_elevation, updated_elevation_unit)[source]¶ +
Function to quickly update all attributes associated with elevation of an HVSRData object
+-
+
- Parameters: +
-
+
- hvsr_dataHVSRData or HVSRBatch
HVSRData or HVSRBatch object containing attributes related to elevation. +If HVSRBatch, updated_surface_elevation should be list or tuple and +updated_elevation_unit may either be str or list/tuple of strings.
+
+- updated_surface_elevationnumbers.Number
Number (float or int) with the updated elevation. +Meters is the preferred unit. If feet are used instead, it will be converted to meters.
+
+- updated_elevation_unitstr
Unit used for updated_surface_elevation. If ‘feet’, it will be converted to meters.
+
+
+- Returns: +
-
+
- HVSRData
HVSRData object with all attributes related to elevation updated
+
+
+
- sprit.x_mark(incolor=False, inTerminal=False)[source]¶ @@ -1876,6 +1968,12 @@
- sprit.sprit_calibration module +
- sprit.sprit_cli module
get_param_docstring()main()
@@ -1935,6 +2033,7 @@
Submodules
remove_outlier_curves() run()test_function()
+update_elevation()- sprit.sprit_jupyter_UI module
-
@@ -1953,6 +2052,8 @@
Submodules
parse_hv_plot_list() parse_plot_string()parse_spec_plot_list()
+plot_cross_section()
+plot_depth_curve()plot_outlier_curves()plot_preview()plot_results()
@@ -1960,7 +2061,16 @@ - sprit.sprit_streamlit_ui module +
- sprit.sprit_streamlit_ui module +
- sprit.sprit_tkinter_ui module
SPRIT_AppSPRIT_App.create_menubar()
@@ -2001,7 +2111,7 @@
Submodules Previous - Next + Next
- +sprit.sprit_calibration.calculate_depth(freq_input, depth_model='ISGS_All', freq_col='Peak', calculate_depth_in_feet=False, calculate_elevation=True, show_depth_curve=True, surface_elevation_data='Elevation', bedrock_elevation_column='BedrockElevation', depth_column='BedrockDepth', verbose=False, export_path=None, swave_velocity=563.0, decimal_places=3, depth_model_in_latex=False, fig=None, ax=None, **kwargs)[source]¶ +
Calculate depth(s) based on a frequency input (usually HVSRData or HVSRBatch oject) and a frequency-depth depth_model (usually a power law relationship).
+-
+
- Parameters: +
-
+
- freq_inputHVSRData, HVSRBatch, float, or filepath, optional
Input with frequency information, by default {sprit_hvsr.HVSRData, sprit_hvsr.HVSRBatch, float, os.PathLike}
+
+- depth_modelstr, tuple, list, or dict, optional
Model describing a relationship between frequency and depth, by default “ISGS_All”
+
+- calculate_depth_in_feetbool, optional
Whether to calculate depth in feet (in addition to meters, which is done by default)
+
+- freq_colstr, optional
Name of the column containing the frequency information of the peak, by default “Peak” (per HVSRData.Table_Report output)
+
+- calculate_elevationbool, optional
Whether or not to calculate elevation, by default True
+
+- surface_elevation_datastr or numeric, optional
The name of the column or a manually specified numeric value to use for the surface elevation value, by default “Elevation”
+
+- bedrock_elevation_columnstr, optional
The name of the column in the TableReport for the bedrock elevation of the point. +This can be either the name of a column in a table (i.e., Table_Report) or a numeric value, by default “BedrockElevation”
+
+- depth_columnstr, optional
_description_, by default “BedrockDepth”
+
+- verbosebool, optional
Whether or not to print information about the processing to the terminal, by default False
+
+- export_path_type_, optional
_description_, by default None
+
+- swave_velocityfloat, optional
Shear wave velocity to use for depth calculations in meters/second, +if using the quarter wavelength shear wave velocity method, by default 563.0
+
+- decimal_placesint, optional
Number of decimal places to round depth results, by default 3
+
+
+- Returns: +
-
+
- HVSRBatch or list if those are input; otherwise, HVSRData object
The returns are the same type as freq_input, except filepath which returns pandas.DataFrame
+
+
+
assert_check()batch_data_read()calculate_azimuth()
+calculate_depth()
+calibrate()catch_errors()check_gui_requirements()check_mark()
@@ -75,6 +77,8 @@
make_it_classy()parse_plot_string()plot_azimuth()
+plot_cross_section()
+plot_depth_curve()plot_hvsr()plot_outlier_curves()plot_preview()
@@ -86,8 +90,10 @@
remove_outlier_curves()run()time_it()
+update_elevation()x_mark()- Submodules
-
+
- sprit.sprit_calibration module
- sprit.sprit_cli module
get_param_docstring()main()
@@ -154,7 +160,7 @@
-
+
-
+
-
+
Submodules¶
-
+
Submodules
read_data()-
diff --git a/docs/sprit.rst b/docs/sprit.rst index 5a45a00..1f8ef33 100644 --- a/docs/sprit.rst +++ b/docs/sprit.rst @@ -12,6 +12,7 @@ Submodules .. toctree:: :maxdepth: 4 + sprit.sprit_calibration sprit.sprit_cli sprit.sprit_hvsr sprit.sprit_jupyter_UI diff --git a/docs/sprit.sprit_calibration.html b/docs/sprit.sprit_calibration.html new file mode 100644 index 0000000..a5de0fe --- /dev/null +++ b/docs/sprit.sprit_calibration.html @@ -0,0 +1,233 @@ + + + + + + +sprit.sprit_calibration module — sprit 2.1-dev documentation + + + + + + + + + + + + + + + + + ++ + ++ + + + \ No newline at end of file diff --git a/docs/sprit.sprit_calibration.rst b/docs/sprit.sprit_calibration.rst new file mode 100644 index 0000000..1ff86db --- /dev/null +++ b/docs/sprit.sprit_calibration.rst @@ -0,0 +1,7 @@ +sprit.sprit\_calibration module +=============================== + +.. automodule:: sprit.sprit_calibration + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/sprit.sprit_cli.html b/docs/sprit.sprit_cli.html index bf61b1d..ec288b0 100644 --- a/docs/sprit.sprit_cli.html +++ b/docs/sprit.sprit_cli.html @@ -4,7 +4,7 @@ -+ + ++++ ++++ ++ +++ + + +sprit.sprit_calibration module¶
+This module will be used for calibration of the ambient HVSR data acquired near wells +to derive a relation between the resonant frequency and the depth to bedrock beneath the subsurface.
+-
+
sprit.sprit_cli module — sprit 2.0 documentation +sprit.sprit_cli module — sprit 2.1-dev documentation @@ -13,14 +13,14 @@ - + - + @@ -50,6 +50,8 @@
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/sprit/sprit_cli.html b/docs/_build/html/_modules/sprit/sprit_cli.html
index 9c4f1ec..e59e601 100644
--- a/docs/_build/html/_modules/sprit/sprit_cli.html
+++ b/docs/_build/html/_modules/sprit/sprit_cli.html
@@ -3,7 +3,7 @@
-
+
+
+
+
+
+
+
+
+
+
+
+
+ Source code for sprit.sprit_calibration
+"""
+This module will be used for calibration of the ambient HVSR data acquired near wells
+to derive a relation between the resonant frequency and the depth to bedrock beneath the subsurface.
+
+"""
+import inspect
+import numbers
+import os
+import pathlib
+import pkg_resources
+import re
+from warnings import warn
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+
+try: # For distribution
+ from sprit import sprit_hvsr
+ from sprit import sprit_plot
+except Exception as e: # For testing
+ import sprit_hvsr
+ import sprit_plot
+
+"""
+Attempt 1: Regression equations:
+
+Load the calibration data as a CSV file. Read in the frequency and the depth to bedrock.
+Use array structures to organize data. The depth should be the independent variable so probably
+the predictor and the frequency is the dependent variable so the response variable.
+
+Two approaches- either use the power law y=ax^b
+or find the least squares solution using the matrix-vector multiplication.
+
+Use GeoPandas to eliminate outliers
+
+calibrate - does calibration
+view_results - produces Pandas dataframe of results
+view_plot - produces calibration curve
+
+
+Things to add:
+- #checkinstance - HVSRData/HVSR Batch
+- #need try-catch blocks while reading in files and checking membership
+- # eliminate outlier points - will have to read in latitude and longitude from spreadsheet and then compare against that of well to find distance in meters
+- #pick only relevant points according to bedrock_type (lithology)
+- #Add calibration equation to get_report csv
+- #Add parameter to sprit.run
+"""
+
+resource_dir = pathlib.Path(pkg_resources.resource_filename(__name__, 'resources/'))
+sample_data_dir = resource_dir.joinpath("sample_data")
+sampleFileName = {'sample_1': sample_data_dir.joinpath("SampleHVSRSite1_2024-06-13_1633-1705.csv")}
+
+def __get_ip_df_params():
+ ip_params = inspect.signature(sprit_hvsr.input_params).parameters
+ fd_params = inspect.signature(sprit_hvsr.fetch_data).parameters
+ return ip_params, fd_params
+
+models = ["ISGS_All", "ISGS_North", "ISGS_Central", "ISGS_Southeast", "ISGS_Southwest",
+ "ISGS_North_Central", "ISGS_SW_SE", "Minnesota_All",
+ "Minnesota_Twin_Cities", "Minnesota_South_Central",
+ "Minnesota_River_Valleys", "Rhine_Graben",
+ "Ibsvon_A", "Ibsvon_B","Delgado_A", "Delgado_B",
+ "Parolai", "Hinzen", "Birgoren", "Ozalaybey", "Harutoonian",
+ "Fairchild", "DelMonaco", "Tun", "Thabet_A", "Thabet_B",
+ "Thabet_C", "Thabet_D"]
+
+swave = ["shear", "swave", "shearwave", "rayleigh", "rayleighwave", "vs"]
+
+model_list = list(map(lambda x : x.casefold(), models))
+
+model_parameters = {"ISGS_All" : (141.81, 1.582), "ISGS_North" : (142.95,1.312), "ISGS_Central" : (119.17, 1.21), "ISGS_Southeast" : (67.973,1.166),
+ "ISGS_Southwest": (61.238,1.003), "ISGS_North_Central" : (117.44, 1.095), "ISGS_SW_SE" : (62.62, 1.039),
+ "Minnesota_All" : (121, 1.323), "Minnesota_Twin_Cities" : (129, 1.295), "Minnesota_South_Central" : (135, 1.248),
+ "Minnesota_River_Valleys" : (83, 1.232), "Rhine_Graben" : (96, 1.388),
+ "Ibsvon_A" : (96, 1.388), "Ibsvon_B" : (146, 1.375), "Delgado_A" : (55.11, 1.256),
+ "Delgado_B" : (55.64, 1.268), "Parolai" : (108, 1.551), "Hinzen" : (137, 1.19), "Birgoren" : (150.99, 1.153),
+ "Ozalaybey" : (141, 1.270), "Harutoonian" : (73, 1.170), "Fairchild" : (90.53, 1), "DelMonaco" : (53.461, 1.01),
+ "Tun" : (136, 1.357), "Thabet_A": (117.13, 1.197), "Thabet_B":(105.14, 0.899), "Thabet_C":(132.67, 1.084), "Thabet_D":(116.62, 1.169)}
+
+
+
+
+
+
+
+[docs]
+def calculate_depth(freq_input,
+ depth_model="ISGS_All",
+ freq_col="Peak",
+ calculate_depth_in_feet=False,
+ calculate_elevation=True,
+ show_depth_curve=True,
+ surface_elevation_data='Elevation',
+ bedrock_elevation_column="BedrockElevation",
+ depth_column="BedrockDepth",
+ verbose=False, # if verbose is True, display warnings otherwise not
+ export_path=None,
+ swave_velocity=563.0,
+ decimal_places=3,
+ depth_model_in_latex=False,
+ fig=None,
+ ax=None,
+ #group_by = "County", -> make a kwarg
+ **kwargs):
+ """Calculate depth(s) based on a frequency input (usually HVSRData or HVSRBatch oject) and a frequency-depth depth_model (usually a power law relationship).
+
+ Parameters
+ ----------
+ freq_input : HVSRData, HVSRBatch, float, or filepath, optional
+ Input with frequency information, by default {sprit_hvsr.HVSRData, sprit_hvsr.HVSRBatch, float, os.PathLike}
+ depth_model : str, tuple, list, or dict, optional
+ Model describing a relationship between frequency and depth, by default "ISGS_All"
+ calculate_depth_in_feet : bool, optional
+ Whether to calculate depth in feet (in addition to meters, which is done by default)
+ freq_col : str, optional
+ Name of the column containing the frequency information of the peak, by default "Peak" (per HVSRData.Table_Report output)
+ calculate_elevation : bool, optional
+ Whether or not to calculate elevation, by default True
+ surface_elevation_data : str or numeric, optional
+ The name of the column or a manually specified numeric value to use for the surface elevation value, by default "Elevation"
+ bedrock_elevation_column : str, optional
+ The name of the column in the TableReport for the bedrock elevation of the point.
+ This can be either the name of a column in a table (i.e., Table_Report) or a numeric value, by default "BedrockElevation"
+ depth_column : str, optional
+ _description_, by default "BedrockDepth"
+ verbose : bool, optional
+ Whether or not to print information about the processing to the terminal, by default False
+ export_path : _type_, optional
+ _description_, by default None
+ swave_velocity : float, optional
+ Shear wave velocity to use for depth calculations in meters/second,
+ if using the quarter wavelength shear wave velocity method, by default 563.0
+ decimal_places : int, optional
+ Number of decimal places to round depth results, by default 3
+
+ Returns
+ -------
+ HVSRBatch or list if those are input; otherwise, HVSRData object
+ The returns are the same type as freq_input, except filepath which returns pandas.DataFrame
+
+ """
+ orig_args = locals()
+ ip_params, fd_params = __get_ip_df_params()
+
+ # Break out if list (of random or not) items
+ if isinstance(freq_input, (list, tuple)):
+ outputList = []
+ for item in freq_input:
+ if 'freq_input' in orig_args:
+ orig_args.pop('freq_input')
+ calc_depth_kwargs = orig_args
+ outputList.append(calculate_depth(freq_input=item, **calc_depth_kwargs))
+ return outputList
+
+ # Break out for Batch data
+ if isinstance(freq_input, sprit_hvsr.HVSRBatch):
+ newBatchList = []
+ # Iterate through each site/HVSRData object and run calculate_depth()
+ for site in freq_input:
+ if 'freq_input' in orig_args:
+ orig_args.pop('freq_input')
+ calc_depth_kwargs = orig_args
+ newBatchList.append(calculate_depth(freq_input=freq_input[site], **calc_depth_kwargs))
+ return sprit_hvsr.HVSRBatch(newBatchList, df_as_read=freq_input.input_df)
+
+ a = 0
+ b = 0
+ params = None
+
+ # Fetch parameters for frequency-depth model
+ if isinstance(depth_model, (tuple, list, dict)):
+ (a, b) = depth_model
+ if a == 0 or b == 0:
+ raise ValueError(f"Model parameters (a, b)={depth_model} cannot be zero, check model inputs.")
+
+ elif isinstance(depth_model, str):
+
+ if depth_model.casefold() in list(map(str.casefold, model_parameters)):
+ for k, v in model_parameters.items():
+ if depth_model.casefold() == k.casefold():
+ (a, b) = v
+ break
+
+ elif depth_model.casefold() in swave:
+ params = depth_model.casefold()
+
+ elif depth_model.casefold() == "all":
+ params = depth_model.casefold()
+
+ else: # parameters a and b could be passed in as a parsable string
+ params = depth_model.split(',')
+ # Work on re update[int(s) for s in re.findall(r"[-+]?(?:\d*\.*\d+)",
+ # depth_model)] #figure this out later for floating points; works for integers
+ (a, b) = params
+ if a == 0 or b == 0:
+ raise ValueError("Parameters cannot be zero, check model inputs")
+
+ # Get frequency input
+ # Checking if freq_input is HVSRData object
+ if isinstance(freq_input, (sprit_hvsr.HVSRData, str, bytes, os.PathLike, float, int)):
+ # Get the table report
+ # If not HVSRData object, let's make a dummy one
+ if not isinstance(freq_input, sprit_hvsr.HVSRData):
+ # Check if freq_input is float/int, convert to HVSRData (use kwargs too)
+ if isinstance(freq_input, (float, int)):
+ if freq_input <= 0:
+ raise ValueError("Peak Frequency cannot be zero or negative")
+
+ if isinstance(surface_elevation_data, numbers.Number):
+ surface_elevation_col = 'Elevation'
+ else:
+ surface_elevation_col = surface_elevation_data
+
+ tableReport = pd.DataFrame(columns=['Site Name',
+ 'Acq_Date',
+ 'XCoord',
+ 'YCoord',
+ surface_elevation_col,
+ freq_col,
+ 'Peak_StDev'
+ 'PeakPasses'])
+ tableReport.loc[0, freq_col] = freq_input
+
+ # Get extra parameters read in via kwargs, if applicable
+ paramDict = {'input_data': "from_user"}
+ if isinstance(surface_elevation_data, numbers.Number):
+ kwargs[surface_elevation_col] = surface_elevation_data
+ surface_elevation_data = 'Elevation'
+
+ for kw, val in kwargs.items():
+ if kw.lower() in [col.lower() for col in tableReport.columns]:
+ colInd = [col.lower() for col in tableReport.columns].index(kw.lower())
+ tableReport.iloc[0, colInd] = val
+
+ if kw in ip_params or kw in fd_params:
+ paramDict[kw] = val
+ paramDict['Table_Report'] = tableReport
+ freq_input = sprit_hvsr.HVSRData(paramDict)
+ # Otherwise, assume it is a file to read in
+ else:
+ if pathlib.Path(freq_input).is_dir():
+ filepathGlob = pathlib.Path(freq_input).glob('*.hvsr')
+ batchList = []
+ for hvsrfile in filepathGlob:
+ batchList.append(sprit_hvsr.import_data(hvsrfile))
+
+ batchArgs = orig_args.copy()
+ try:
+ del batchArgs['freq_input']
+ except KeyError:
+ pass
+
+ hvDataOutList = []
+ for hvData in batchList:
+ hvDataOutList.append(calculate_depth(freq_input=hvData,
+ **batchArgs))
+ return sprit_hvsr.HVSRBatch(hvDataOutList)
+ # First, check if it is a filepath
+ freqDataPath = pathlib.Path(freq_input)
+ if not freqDataPath.exists():
+ raise RuntimeError(f"Specified filepath for frequency data does not exist: freq_input={freq_input}")
+
+ if 'hvsr' not in freqDataPath.suffix.lower():
+ if verbose:
+ print('Assuming file is a table readable by pandas.read_csv(), with column containing frequency data specified by freq_col={freq_col}')
+ tableReport = pd.read_csv(freqDataPath)
+
+ # Get parameters from table
+ param_dict_list = [{'input_data': freq_input,
+ "Table_Report": tableReport}] * tableReport.shape[0]
+
+ # Get parameters directly from table
+ tableCols = tableReport.columns
+ for col in tableCols:
+ if col.lower() in ip_params or col.lower() in fd_params:
+ for i, (ind, row) in enumerate(tableReport.iterrows()):
+ param_dict_list[i][col.lower()] = row[col]
+
+ # Get/overwrite table parameters with directly input parameters
+ hvdList = []
+ for parDict in param_dict_list:
+ for kw, val in kwargs.items():
+ if kw in ip_params or kw in fd_params:
+ parDict[kw] = val
+ hvdList.append(sprit_hvsr.HVSRData(parDict))
+
+ # Either make HVSRData or HVSRBatch object
+ if len(hvdList) > 1:
+ freq_input = sprit_hvsr.HVSRBatch(hvdList, df_as_read=pd.DataFrame(param_dict_list))
+ else:
+ freq_input = hvdList[0]
+
+ else:
+ if verbose:
+ print('Assuming file with .*hvsr* suffix is an HVSR data file created by SpRIT.')
+ freq_input = sprit_hvsr.import_data(freqDataPath)
+ tableReport = freq_input.Table_Report
+
+ if isinstance(freq_input, sprit_hvsr.HVSRData):
+ if not hasattr(freq_input, 'Table_Report'):
+ if verbose:
+ warn("Passed HVSRData Object has no attribute Table_Report, attempting to generate one.")
+ tableReport = sprit_hvsr.get_report(freq_input, report_format='csv')
+ else:
+ tableReport = freq_input.Table_Report
+
+ # Break out for Batch data (in case it was generated during readin of file, for example)
+ if isinstance(freq_input, sprit_hvsr.HVSRBatch):
+ newBatchList = []
+ # Iterate through each site/HVSRData object and run calculate_depth()
+ for site in freq_input:
+ if 'freq_input' in orig_args:
+ orig_args.pop('freq_input')
+ calc_depth_kwargs = orig_args
+ newBatchList.append(calculate_depth(freq_input=freq_input[site], **calc_depth_kwargs))
+ return sprit_hvsr.HVSRBatch(newBatchList, df_as_read=freq_input.input_df)
+
+ # Calibrate data
+ pf_values = tableReport[freq_col].values
+
+ calib_data = []
+ depthModelList = []
+ depthModelTypeList = []
+
+ for site_peak_freq in pf_values:
+ try:
+ if depth_model in swave:
+ calib_data.append(swave_velocity/(4*site_peak_freq))
+
+ if depth_model_in_latex:
+ dModelStr = f"$\\frac{{{swave_velocity}}}{{4\\times{site_peak_freq}}}$"
+ else:
+ dModelStr = f"{swave_velocity}/(4 * {site_peak_freq})"
+ depthModelList.append(dModelStr)
+ depthModelTypeList.append('Quarter Wavelength')
+ else:
+ if depth_model == "all":
+ a_list = []
+ b_list = []
+ for name, model_params in model_parameters.items():
+ a_list.append(model_params[0])
+ b_list.append(model_params[1])
+ (a, b) = (np.nanmean(a_list), np.nanmean(b_list))
+
+ calib_data.append(a*(site_peak_freq**-b))
+ if hasattr(freq_input, 'x_freqs'):
+ freq_input['x_depth_m'] = {'Z': np.around([a*(f**-b) for f in freq_input["x_freqs"]['Z']], decimal_places),
+ 'E': np.around([a*(f**-b) for f in freq_input["x_freqs"]['E']], decimal_places),
+ 'N': np.around([a*(f**-b) for f in freq_input["x_freqs"]['N']], decimal_places)}
+
+ # Calculate depth in feet
+ freq_input['x_depth_ft'] = {'Z': np.around(freq_input['x_depth_m']['Z']*3.281, decimal_places),
+ 'E': np.around(freq_input['x_depth_m']['E']*3.281, decimal_places),
+ 'N': np.around(freq_input['x_depth_m']['N']*3.281, decimal_places)}
+
+ if depth_model_in_latex:
+ dModelStr = f"{a} \\times {{{site_peak_freq}}}^{{-{b}}}"
+ else:
+ dModelStr = f"{a} * {site_peak_freq}^-{b}"
+ depthModelList.append(dModelStr)
+ depthModelTypeList.append('Power Law')
+
+ except Exception as e:
+ raise ValueError("Error in calculating depth, check HVSRData object for empty values or missing columns") from e
+
+ # Record depth data in table
+ tableReport[depth_column] = np.around(calib_data, decimal_places)
+
+ # Calculate elevation data
+ if calculate_elevation and surface_elevation_data in tableReport.columns:
+ tableReport[bedrock_elevation_column] = (tableReport[surface_elevation_data] - tableReport[depth_column]).round(decimal_places)
+ if hasattr(freq_input, 'x_depth_m'):
+ freq_input['x_elev_m'] = {'Z': np.around([tableReport[surface_elevation_data].values[0] - f for f in freq_input["x_depth_m"]['Z']], decimal_places),
+ 'E': np.around([tableReport[surface_elevation_data].values[0] - f for f in freq_input["x_depth_m"]['E']], decimal_places),
+ 'N': np.around([tableReport[surface_elevation_data].values[0] - f for f in freq_input["x_depth_m"]['N']], decimal_places)}
+
+ if calculate_depth_in_feet:
+ tableReport[depth_column+'_ft'] = np.around(calib_data*3.281,
+ decimals=decimal_places)
+ if calculate_elevation and surface_elevation_data in tableReport.columns:
+ tableReport[bedrock_elevation_column+'_ft'] = np.around(tableReport[bedrock_elevation_column] * 3.281,
+ decimals=decimal_places)
+ if hasattr(freq_input, 'x_elev_m') and not hasattr(freq_input['x_depth_ft']):
+ # Calculate depth in feet
+ freq_input['x_depth_ft'] = {'Z': np.around(freq_input['x_depth_m']['Z']*3.281, decimal_places),
+ 'E': np.around(freq_input['x_depth_m']['E']*3.281, decimal_places),
+ 'N': np.around(freq_input['x_depth_m']['N']*3.281, decimal_places)}
+
+ tableReport["DepthModel"] = depthModelList
+ tableReport["DepthModelType"] = depthModelTypeList
+
+ # Do plotting work
+ if fig is None and ax is None:
+ fig, ax = plt.subplots()
+ elif fig is not None:
+ ax = fig.get_axes()
+ if len(ax) == 1:
+ ax = ax[0]
+
+ pdc_kwargs = {k: v for k, v in kwargs.items() if k in tuple(inspect.signature(sprit_plot.plot_depth_curve).parameters.keys())}
+ freq_input = sprit_plot.plot_depth_curve(hvsr_results=freq_input,
+ show_depth_curve=show_depth_curve,
+ fig=fig, ax=ax, **pdc_kwargs)
+
+ plt.sca(ax)
+ if show_depth_curve:
+ plt.show()
+ else:
+ plt.close()
+
+ # Export as specified
+ if export_path is not None and os.path.exists(export_path):
+ if export_path == freq_input:
+ tableReport.to_csv(freq_input)
+ if verbose:
+ print("Saving data in the original file")
+
+ else:
+ if "/" in export_path:
+ temp = os.path.join(export_path+ "/"+ site + ".csv")
+ tableReport.to_csv(temp)
+
+ else:
+ temp = os.path.join(export_path+"\\"+ site + ".csv")
+ tableReport.to_csv(temp)
+
+ if verbose:
+ print("Saving data to the path specified")
+
+ freq_input.Table_Report = tableReport
+ return freq_input
+ else:
+ raise RuntimeError(f"The freq_input parameter is not the correct type:\n\ttype(freq_input)={type(freq_input)}")
+
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+
+[docs]
+def calibrate(calib_filepath, calib_type = "power",outlier_radius = None, bedrock_type = None,peak_freq_col = "PeakFrequency",
+ bed_depth_col = "Bedrock_Depth", **kwargs):
+
+ calib_data = None
+
+ calib_types = ["Power", "swave_velocity", "Matrix"]
+
+ calib_type_list = list(map(lambda x : x.casefold(), calib_types))
+
+ power_list = ["Power", "power", "pw", "POWER"]
+
+ Vs_list = ["vs", "VS", "v_s", "V_s", "V_S"]
+
+ matrix_list = ["matrix", "Matrix", "MATRIX"]
+
+
+ bedrock_types = ["shale", "limetone", "dolomite",
+ "sedimentary", "igneous", "metamorphic"]
+
+
+
+
+ freq_columns_names = ["PeakFrequency", "ResonanceFrequency", "peak_freq", "res_freq", "Peakfrequency", "Resonancefrequency", "PF", "RF", "pf", "rf"]
+
+ bedrock_depth_names = ["BedrockDepth", "DepthToBedrock", "bedrock_depth", "depth_bedrock", "depthtobedrock", "bedrockdepth"]
+
+
+ # if calib_type.casefold() in calib_type_list:
+
+
+ # if calib_type.casefold() in power_list:
+
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+Source code for sprit.sprit_hvsr
import pathlib
import pickle
import pkg_resources
+import re
import struct
import sys
import tempfile
@@ -126,8 +127,9 @@ Source code for sprit.sprit_hvsr
DEFAULT_PLOT_STR = "HVSR p ann COMP+ p ann SPEC p ann"
OBSPY_FORMATS = ['AH', 'ALSEP_PSE', 'ALSEP_WTH', 'ALSEP_WTN', 'CSS', 'DMX', 'GCF', 'GSE1', 'GSE2', 'KINEMETRICS_EVT', 'KNET', 'MSEED', 'NNSA_KB_CORE', 'PDAS', 'PICKLE', 'Q', 'REFTEK130', 'RG16', 'SAC', 'SACXY', 'SEG2', 'SEGY', 'SEISAN', 'SH_ASC', 'SLIST', 'SU', 'TSPAIR', 'WAV', 'WIN', 'Y']
+
# Resources directory path, and the other paths as well
-RESOURCE_DIR = pathlib.Path(pkg_resources.resource_filename(__name__, 'resources/'))
+RESOURCE_DIR = pathlib.PurePath(pkg_resources.resource_filename(__name__, 'resources'))
SAMPLE_DATA_DIR = RESOURCE_DIR.joinpath('sample_data')
SETTINGS_DIR = RESOURCE_DIR.joinpath('settings')
@@ -175,10 +177,10 @@ Source code for sprit.sprit_hvsr
'sample_7':SAMPLE_DATA_DIR.joinpath('SampleHVSRSite7_BNE_4_AM.RAC84.00.2023.191_2023-07-10_2237-2259.MSEED'),
'sample_8':SAMPLE_DATA_DIR.joinpath('SampleHVSRSite8_BNE_6_AM.RAC84.00.2023.191_2023-07-10_1806-1825.MSEED'),
'sample_9':SAMPLE_DATA_DIR.joinpath('SampleHVSRSite9_BNE-2_AM.RAC84.00.2023.192_2023-07-11_0000-0011.MSEED'),
- 'sample_10':SAMPLE_DATA_DIR.joinpath('SampleHVSRSite10_BNE_4_AM.RAC84.00.2023.191_2023-07-10_2237-2259.MSEED'),
+ 'sample_10': SAMPLE_DATA_DIR.joinpath('SampleHVSRSite10_BNE_4_AM.RAC84.00.2023.191_2023-07-10_2237-2259.MSEED'),
- 'batch':SAMPLE_DATA_DIR.joinpath('Batch_SampleData.csv')}
-
+ 'batch': SAMPLE_DATA_DIR.joinpath('Batch_SampleData.csv'),
+ 'sample_batch': SAMPLE_DATA_DIR.joinpath('Batch_SampleData.csv')}
# CLASSES
# Check if the data is already the right class
@@ -215,25 +217,78 @@ Source code for sprit.sprit_hvsr
"""
@check_instance
- def __init__(self, batch_dict):
+ def __init__(self, batch_input, batch_ext=None, df_as_read=None):
"""HVSR Batch initializer
Parameters
----------
- batch_dict : dict
+ batch_input : dict, list, or tuple
Dictionary containing Key value pairs with {sitename: HVSRData object}
"""
- self._batch_dict = batch_dict
- self.batch_dict = self._batch_dict
+ if isinstance(batch_input, HVSRBatch):
+ return batch_input
+
+ self._batch_input = batch_input
+ self.batch_input = self._batch_input
+
+ self._batch_dict = self.batch_dict = {}
+
+ self._input_df = df_as_read
+ self.input_df = self._input_df
+
self.batch = True
- for sitename, hvsrdata in batch_dict.items():
+ if isinstance(batch_input, (list, tuple,)):
+ siteNo = 0
+ zfilldigs = len(str(len(batch_input)))
+
+ for hvdata in batch_input:
+ if hasattr(hvdata, 'site'):
+ sitename = hvdata.site
+ elif hasattr(hvdata, 'Table_Report') and 'Site Name' in hvdata.Table_Report.columns:
+ sitename = hvdata.Table_Report['Site Name'][0]
+ else:
+ sitename = f"HVSRSite{str(siteNo).zfill(zfilldigs)}"
+
+ self.batch_dict[sitename] = hvdata
+ elif isinstance(batch_input, dict):
+ self.batch_dict = batch_input
+ elif isinstance(batch_input, HVSRData):
+ self.batch_dict[batch_input['site']] = batch_input
+ elif pathlib.Path(batch_input).exists():
+ if pathlib.Path(batch_input).is_dir():
+ if batch_ext is not None:
+ batchfileglob = pathlib.Path(batch_input).glob("*"+batch_ext)
+ batchfiledict = {}
+ if 'hvsr' in batch_ext:
+ for hvfile in batchfileglob:
+ currhvfile = import_data(hvfile)
+ batchfiledict[currhvfile['site']] = currhvfile
+ self.batch_dict = self._batch_dict = batchfiledict
+ else:
+ batchfileglob = []
+ batchfiledict = {}
+ for ftype in OBSPY_FORMATS:
+ batchfileglob.extend(pathlib.Path(batch_input).glob("*"+ftype))
+ for hvfile in batchfileglob:
+ currhvfile = import_data(hvfile)
+ batchfiledict[currhvfile['site']] = currhvfile
+ self.batch_dict = self._batch_dict = batchfiledict
+ else:
+ # Read the batch file in and return it
+ return import_data(batch_input)
+ else:
+ raise TypeError(f"The batch_input parameter of the HVSRBatch class must be a dict of paramteres, list or tuple of HVSRData obejcts, or an HVSRData object itself. {type(batch_input)}")
+
+
+ self._batch_dict = self.batch_dict
+ for sitename, hvsrdata in self.batch_dict.items():
setattr(self, sitename, hvsrdata)
- self[sitename]['batch'] = True
- self.sites = list(self._batch_dict.keys())
+ self[sitename]['batch'] = True
+ self.sites = list(self.batch_dict.keys())
- #METHODS
+ # METHODS
def __to_json(self, filepath):
"""Not yet implemented, but may allow import/export to json files in the future, rather than just .hvsr pickles
@@ -300,9 +355,9 @@ Source code for sprit.sprit_hvsr
"""
if type.lower()=='deep':
- return HVSRBatch(copy.deepcopy(self._batch_dict))
+ return HVSRBatch(copy.deepcopy(self._batch_dict), df_as_read=self._input_df)
else:
- return HVSRBatch(copy.copy(self._batch_dict))
+ return HVSRBatch(copy.copy(self._batch_dict), df_as_read=self._input_df)
#Method wrapper of sprit.plot_hvsr function
@@ -732,7 +787,7 @@ Source code for sprit.sprit_hvsr
"""
browserList = ['browser', 'remi', 'default', 'd']
windowList = ['windowed', 'window', 'qt', 'tkinter', 'tk']
- widgetList = ['widget', 'jupyter', 'notebook', 'w', 'nb']
+ widgetList = ['widget', 'jupyter', 'notebook', 'nb']
liteList = ['lite', 'light', 'basic', 'l', 'b']
if kind.lower() in browserList:
@@ -955,6 +1010,7 @@ Source code for sprit.sprit_hvsr
raise RuntimeError('Data not read correctly, see sprit.fetch_data() function and parameters for more details.')
# BREAK OUT FOR BATCH PROCESSING
+ run_kwargs_for_df = []
if isinstance(hvsrDataIN, HVSRBatch):
# Create dictionary that will be used to create HVSRBatch object
@@ -962,7 +1018,7 @@ Source code for sprit.sprit_hvsr
# Loop through each site and run sprit.run() for each HVSRData object
for site_name, site_data in hvsrDataIN.items():
- run_kwargs = {}#orig_args.copy() # Make a copy so we don't accidentally overwrite
+ run_kwargs = {} #orig_args.copy() # Make a copy so we don't accidentally overwrite
print(f'\n\n**PROCESSING DATA FOR SITE {site_name.upper()}**\n')
run_kwargs['input_data'] = site_data
@@ -988,14 +1044,38 @@ Source code for sprit.sprit_hvsr
try:
hvsrBatchDict[site_name] = run(**run_kwargs)
+ run_kwargs_for_df.append(run_kwargs)
except Exception as e:
- sprit_utils._get_error_from_exception(e)
-
hvsrBatchDict[site_name] = site_data
- hvsrBatchDict[site_name]['ProcessingStatus']['PPSDStatus']=False
+ hvsrBatchDict[site_name]['Error_Message'] = sprit_utils._get_error_from_exception(e,
+ print_error_message=False,
+ return_error_message=True)
+ if verbose:
+ sprit_utils._get_error_from_exception(e)
+
+ print(f"Error processing site {site_name}. Continuing processing of remaining sites.")
+
+ hvsrBatchDict[site_name]['ProcessingStatus']['PPSDStatus'] = False
hvsrBatchDict[site_name]['ProcessingStatus']['OverallStatus'] = False
-
- return HVSRBatch(hvsrBatchDict)
+
+ # Create batch object
+ hvsrBatchData = HVSRBatch(hvsrBatchDict, df_as_read=pd.DataFrame(run_kwargs_for_df))
+
+ # Use batch object to get Output Table with all data, including results and inputs
+ for s, site in enumerate(hvsrBatchData):
+ if hasattr(hvsrBatchData[site], 'Table_Report'):
+ if s == 0:
+ table_reports = hvsrBatchData[site].Table_Report
+ else:
+ table_reports = pd.concat([table_reports, hvsrBatchData[site].Table_Report])
+ else:
+ if s == 0:
+ table_reports = pd.DataFrame()
+
+ hvsrBatchData['Table_Report'] = pd.merge(left=hvsrBatchData.input_df, right=table_reports,
+ how='outer',
+ left_on='site', right_on='Site Name')
+ return hvsrBatchData
# Calculate azimuths
hvsr_az = hvsrDataIN
@@ -1090,8 +1170,9 @@ Source code for sprit.sprit_hvsr
else:
errMsg = e
- print(f"Error during generate_psds() for {site_name}: \n{errMsg}")
- if source == 'file' or source == 'raw':
+ if verbose:
+ print(f"Error during generate_psds() for {site_name}: \n{errMsg}")
+ if (source == 'file' or source == 'raw') and verbose:
raise RuntimeError(f"generate_psds() error: {errMsg}")
# Reformat data so HVSRData and HVSRBatch data both work here
@@ -1150,17 +1231,12 @@ Source code for sprit.sprit_hvsr
process_hvsr_kwargs = {k: v for k, v in kwargs.items() if k in tuple(inspect.signature(process_hvsr).parameters.keys())}
hvsr_results = process_hvsr(hvsr_data=psd_data, verbose=verbose, **process_hvsr_kwargs)
except Exception as e:
- traceback.print_exception(sys.exc_info()[1])
- exc_type, exc_obj, tb = sys.exc_info()
- f = tb.tb_frame
- lineno = tb.tb_lineno
- filename = f.f_code.co_filename
- errLineNo = str(traceback.extract_tb(sys.exc_info()[2])[-1].lineno)
- error_category = type(e).__name__.title().replace('error', 'Error')
- error_message = f"{e} ({errLineNo})"
- print(f"{error_category} ({errLineNo}): {error_message}")
- print(lineno, filename, f)
+ print_error = False
+ if verbose:
+ print_error = True
+ #sprit_utils._get_error_from_exception(e,
+ # print_error_message=print_error)
if isinstance(hvsr_results, HVSRData):
hvsr_results = {hvsr_results['site']: hvsr_results}
@@ -1230,7 +1306,8 @@ Source code for sprit.sprit_hvsr
# Add azimuth as a requested plot if azimuthal data exists but not requested in plot
if not az_requested and hasAz and hvsr_results.horizontal_method != 'Single Azimuth':
get_report_kwargs['plot_type'] = get_report_kwargs['plot_type'] + ' az'
- get_report(hvsr_results=hvsr_results, verbose=verbose, **get_report_kwargs)
+
+ hvsr_results = get_report(hvsr_results=hvsr_results, verbose=verbose, **get_report_kwargs)
if verbose:
if 'report_formats' in get_report_kwargs.keys():
@@ -1338,22 +1415,25 @@ Source code for sprit.sprit_hvsr
'process_hvsr_params': process_hvsr_params,
'check_peaks_params': check_peaks_params,
'get_report_params': get_report_params}
-
- # Get a list of all functions (for which paramters are used) in sprit.run()
- run_functions_list = [input_params, fetch_data,
- get_metadata, calculate_azimuth,
- remove_noise, generate_psds, remove_outlier_curves,
- process_hvsr, check_peaks,
- get_report, export_data]
-
+
+ def __get_run_functions():
+ # Get a list of all functions (for which paramters are used) in sprit.run()
+ run_functions_list = [input_params, fetch_data, batch_data_read,
+ get_metadata, calculate_azimuth,
+ remove_noise, generate_psds, remove_outlier_curves,
+ process_hvsr, check_peaks,
+ get_report, export_data]
+
+ return run_functions_list
+ SPRIT_RUN_FUNCTIONS = __get_run_functions()
# Get default values of all functions in a dict
default_dict = {}
- for i, fun in enumerate(run_functions_list):
+ for i, fun in enumerate(SPRIT_RUN_FUNCTIONS):
for param_name, param_info in inspect.signature(fun).parameters.items():
if param_info.default is not inspect._empty:
default_dict[param_name] = param_info.default
-
- if batch_type == 'sample':
+
+ if batch_type == 'sample' or batch_data in sampleFileKeyMap.keys():
sample_data = True
batch_type = 'table'
else:
@@ -1363,10 +1443,17 @@ Source code for sprit.sprit_hvsr
stream_dict = {}
data_dict = {}
if batch_type == 'table':
- if isinstance(batch_data, pd.DataFrame):
+ # If this is sample data, we need to create absolute paths to the filepaths
+ if sample_data:
+ #SAMPLE_DATA_DIR = pathlib.Path(pkg_resources.resource_filename(__name__, 'resources/sample_data/'))
+ dataReadInfoDF = pd.read_csv(sampleFileKeyMap['sample_batch'])
+ for index, row in dataReadInfoDF.iterrows():
+ dataReadInfoDF.loc[index, 'input_data'] = SAMPLE_DATA_DIR.joinpath(row.loc['input_data'])
+ elif isinstance(batch_data, pd.DataFrame):
dataReadInfoDF = batch_data
elif isinstance(batch_data, dict):
# For params input
+ dataReadInfoDF = pd.DataFrame.from_dict(batch_data)
pass
else: # Read csv
read_csv_kwargs = {k: v for k, v in locals()['readcsv_getMeta_fetch_kwargs'].items() if k in inspect.signature(pd.read_csv).parameters}
@@ -1374,12 +1461,6 @@ Source code for sprit.sprit_hvsr
if 'input_data' in dataReadInfoDF.columns:
filelist = list(dataReadInfoDF['input_data'])
- # If this is sample data, we need to create absolute paths to the filepaths
- if sample_data:
- SAMPLE_DATA_DIR = pathlib.Path(pkg_resources.resource_filename(__name__, 'resources/sample_data/'))
- for index, row in dataReadInfoDF.iterrows():
- dataReadInfoDF.loc[index, 'input_data'] = SAMPLE_DATA_DIR.joinpath(row.loc['input_data'])
-
# Generate site names if they don't exist already
if 'site' not in dataReadInfoDF.columns:
siterows = []
@@ -1427,6 +1508,8 @@ Source code for sprit.sprit_hvsr
print('Fetching the following files:')
+ # Get processing parameters, either from column param_col or from individual columns
+ # If param_col, format is string of format: "param_name=param_val, param_name2=param_val2"
param_dict_list = []
verboseStatement = []
if param_col is None: # Not a single parameter column, each col=parameter
@@ -1434,7 +1517,7 @@ Source code for sprit.sprit_hvsr
param_dict = {}
verboseStatement.append([])
for col in dataReadInfoDF.columns:
- for fun in run_functions_list:
+ for fun in SPRIT_RUN_FUNCTIONS:
if col in inspect.signature(fun).parameters:
currParam = dataReadInfoDF.loc[row_ind, col]
if pd.isna(currParam) or currParam == 'nan':
@@ -1468,6 +1551,7 @@ Source code for sprit.sprit_hvsr
if batch_params is None:
batch_params = [{}] * len(batch_data)
+ # Get batch_parameters
if isinstance(batch_params, list):
if len(batch_params) != len(batch_data):
raise RuntimeError('If batch_params is list, it must be the same length as batch_data. len(batch_params)={} != len(batch_data)={}'.format(len(batch_params), len(batch_data)))
@@ -1481,17 +1565,21 @@ Source code for sprit.sprit_hvsr
# Read and process each MiniSEED file
for i, file in enumerate(batch_data):
param_dict_list[i]['input_data'] = file
-
- hvsr_metaDict = {}
+
+ # Get a uniformly formatted input DataFrame
+ input_df_uniformatted = pd.DataFrame(param_dict_list)
+
+ # Do batch fun of input_params() and fetch_data() (these are skipped in run() if batch mode is used)
+ hvsr_batchDict = {}
zfillDigs = len(str(len(param_dict_list))) # Get number of digits of length of param_dict_list
i = 0
- for i, param_dict in enumerate(param_dict_list):
+ for i, param_dict in enumerate(param_dict_list):
# Read the data file into a Stream object
input_params_kwargs = {k: v for k, v in locals()['readcsv_getMeta_fetch_kwargs'].items() if k in inspect.signature(input_params).parameters}
input_params_kwargs2 = {k: v for k, v in param_dict.items() if k in inspect.signature(input_params).parameters}
input_params_kwargs.update(input_params_kwargs2)
- # Run input_params
+ # Run input_params()
try:
ipverboseString = '\tinput_params: <No parameters specified>, '
for arg, value in input_params_kwargs.items():
@@ -1502,10 +1590,13 @@ Source code for sprit.sprit_hvsr
params = input_params(**input_params_kwargs)
except Exception as e:
+ params = input_params_kwargs
+ params['ProcessingStatus'] = {}
params['ProcessingStatus']['InputParamsStatus'] = False
params['ProcessingStatus']['OverallStatus'] = False
verboseStatement.append(f"\t{e}")
+ # Run fetch_data()
fetch_data_kwargs = {k: v for k, v in locals()['readcsv_getMeta_fetch_kwargs'].items() if k in inspect.signature(fetch_data).parameters}
fetch_data_kwargs2 = {k: v for k, v in param_dict.items() if k in inspect.signature(fetch_data).parameters}
fetch_data_kwargs.update(fetch_data_kwargs2)
@@ -1520,6 +1611,7 @@ Source code for sprit.sprit_hvsr
hvsrData = fetch_data(params=params, **fetch_data_kwargs)
except Exception as e:
+ hvsrData = params
hvsrData['ProcessingStatus']['FetchDataStatus'] = False
hvsrData['ProcessingStatus']['OverallStatus'] = False
verboseStatement.append(f"\t{e}")
@@ -1556,22 +1648,23 @@ Source code for sprit.sprit_hvsr
if 'processing_parameters' in hvsrData.keys():
processing_parameters = hvsrData['processing_parameters'].copy()
else:
- processing_parameters = {} #"input_params": input_params_kwargs, "fetch_data": fetch_data_kwargs}
+ processing_parameters = {} # "input_params": input_params_kwargs, "fetch_data": fetch_data_kwargs}
- for fun in run_functions_list:
+ for fun in SPRIT_RUN_FUNCTIONS:
specified_params = {k: v for k, v in param_dict.items() if k in inspect.signature(fun).parameters}
processing_parameters[fun.__name__] = specified_params
+ # Assume source is 'file' if not specified
hvsrData['processing_parameters'] = processing_parameters
if 'source' not in hvsrData['processing_parameters']['fetch_data'].keys():
hvsrData['processing_parameters']['fetch_data']['source'] = 'file'
- hvsr_metaDict[hvsrData['site']] = hvsrData
+ hvsr_batchDict[hvsrData['site']] = hvsrData
- hvsrBatch = HVSRBatch(hvsr_metaDict)
+ hvsrBatch = HVSRBatch(hvsr_batchDict, df_as_read=input_df_uniformatted)
print()
- print('Finished reading input data in preparation of batch processing')
+ print('Finished reading input data in preparation for batch processing')
return hvsrBatch
@@ -1650,7 +1743,7 @@ Source code for sprit.sprit_hvsr
print()
if isinstance(hvsr_data, HVSRBatch):
- #If running batch, we'll loop through each site
+ # If running batch, we'll loop through each site
hvsr_out = {}
for site_name in hvsr_data.keys():
args = orig_args.copy() #Make a copy so we don't accidentally overwrite
@@ -1668,7 +1761,7 @@ Source code for sprit.sprit_hvsr
hvsr_data[site_name]['ProcessingStatus']['OverallStatus'] = False
hvsr_out = hvsr_data
- output = HVSRBatch(hvsr_out)
+ output = HVSRBatch(hvsr_out, df_as_read=hvsr_data.input_df)
return output
elif isinstance(hvsr_data, (HVSRData, dict, obspy.Stream)):
@@ -1881,7 +1974,7 @@ Source code for sprit.sprit_hvsr
else:
warnings.warn(f"\t{site_name}: check_peaks() unsuccessful. Peaks not checked.", RuntimeWarning)
- hvsr_data = HVSRBatch(hvsr_data)
+ hvsr_data = HVSRBatch(hvsr_data, df_as_read=hvsr_data.input_df)
else:
HVColIDList = ['_'.join(col_name.split('_')[2:]) for col_name in hvsr_data['hvsr_windows_df'].columns if col_name.startswith('HV_Curves') and 'Log' not in col_name]
HVColIDList[0] = 'HV'
@@ -1935,7 +2028,7 @@ Source code for sprit.sprit_hvsr
peak_freq_range = hvsr_data['peak_freq_range']
# Do for hvsr
- peak = __init_peaks(x, y, index_list, hvsr_band, peak_freq_range)
+ peak = __init_peaks(x, y, index_list, hvsr_band, peak_freq_range, _min_peak_amp=0.5)
peak = __check_curve_reliability(hvsr_data, peak, col_id)
peak = __check_clarity(x, y, peak, do_rank=True)
@@ -1947,7 +2040,7 @@ Source code for sprit.sprit_hvsr
else:
index_p = list()
- peakp = __init_peaks(x, hvsrp, index_p, hvsr_band, peak_freq_range)
+ peakp = __init_peaks(x, hvsrp, index_p, hvsr_band, peak_freq_range, _min_peak_amp=1)
peakp = __check_clarity(x, hvsrp, peakp, do_rank=True)
# Do for hvsrm
@@ -1957,12 +2050,12 @@ Source code for sprit.sprit_hvsr
else:
index_m = list()
- peakm = __init_peaks(x, hvsrm, index_m, hvsr_band, peak_freq_range)
+ peakm = __init_peaks(x, hvsrm, index_m, hvsr_band, peak_freq_range, _min_peak_amp=0)
peakm = __check_clarity(x, hvsrm, peakm, do_rank=True)
# Get standard deviation of time peaks
stdf = __get_stdf(x, index_list, hvsrPeaks)
-
+
peak = __check_freq_stability(peak, peakm, peakp)
peak = __check_stability(stdf, peak, hvsr_log_std, rank=True)
@@ -2527,7 +2620,7 @@ Source code for sprit.sprit_hvsr
params['input_data'][i] = sprit_utils.checkifpath(str(d).strip(), sample_list=SAMPLE_LIST)
dPath = params['input_data']
elif isinstance(params['input_data'], (obspy.Stream, obspy.Trace)):
- pass
+ dPath = pathlib.Path() #params['input_data']
elif isinstance(params['input_data'], HVSRData):
dPath = pathlib.Path(params['input_data']['input_data'])
if not isinstance(params['input_data']['stream'], (obspy.Stream, obspy.Trace)):
@@ -2670,7 +2763,7 @@ Source code for sprit.sprit_hvsr
rawDataIN = obspy.Stream(stream) #Just in case
else:
rawDataIN = rawDataIN + stream #This adds a stream/trace to the current stream object
- elif str(dPath)[:6].lower()=='sample':
+ elif str(dPath)[:6].lower() == 'sample':
pass
else:
rawDataIN = obspy.read(dPath, **obspyReadKwargs)#, starttime=obspy.core.UTCDateTime(params['starttime']), endttime=obspy.core.UTCDateTime(params['endtime']), nearest_sample =True)
@@ -2683,24 +2776,27 @@ Source code for sprit.sprit_hvsr
print('\nFetching data (fetch_data())')
batch_data_read_kwargs = {k: v for k, v in kwargs.items() if k in tuple(inspect.signature(batch_data_read).parameters.keys())}
params = batch_data_read(batch_data=params['input_data'], verbose=verbose, **batch_data_read_kwargs)
- params = HVSRBatch(params)
+ params = HVSRBatch(params, df_as_read=params.input_df)
return params
elif str(params['input_data']).lower() in SAMPLE_LIST or f"sample{params['input_data'].lower()}" in SAMPLE_LIST:
SAMPLE_DATA_DIR = pathlib.Path(pkg_resources.resource_filename(__name__, 'resources/sample_data/'))
if source=='batch':
params['input_data'] = SAMPLE_DATA_DIR.joinpath('Batch_SampleData.csv')
params = batch_data_read(batch_data=params['input_data'], batch_type='sample', verbose=verbose)
- params = HVSRBatch(params)
+ params = HVSRBatch(params, df_as_read=params.input_df)
return params
elif source=='dir':
params['input_data'] = SAMPLE_DATA_DIR.joinpath('Batch_SampleData.csv')
params = batch_data_read(batch_data=params['input_data'], batch_type='sample', verbose=verbose)
- params = HVSRBatch(params)
+ params = HVSRBatch(params, df_as_read=params.input_df)
return params
elif source=='file':
params['input_data'] = str(params['input_data']).lower()
if params['input_data'].lower() in sampleFileKeyMap.keys():
+ if params['input_data'].lower() == 'sample':
+ params['input_data'] = sampleFileKeyMap
+
params['input_data'] = sampleFileKeyMap[params['input_data'].lower()]
else:
params['input_data'] = SAMPLE_DATA_DIR.joinpath('SampleHVSRSite1_AM.RAC84.00.2023.046_2023-02-15_1704-1734.MSEED')
@@ -3920,7 +4016,7 @@ Source code for sprit.sprit_hvsr
# Import data
[docs]
-def import_data(import_filepath, data_format='pickle'):
+def import_data(import_filepath, data_format='pickle', show_data=False):
"""Function to import .hvsr (or other extension) data exported using export_data() function
Parameters
@@ -3934,11 +4030,23 @@ Source code for sprit.sprit_hvsr
-------
HVSRData or HVSRBatch object
"""
- if data_format=='pickle':
+
+ sample_list = ['sample', 'sampledata', 's']
+ if import_filepath in sample_list:
+ import_filepath = RESOURCE_DIR.joinpath(r'sample_data')
+ import_filepath = import_filepath.joinpath(r'SampleHVSRSite01.hvsr')
+
+ if data_format == 'pickle':
with open(import_filepath, 'rb') as f:
dataIN = pickle.load(f)
+ elif data_format.lower() == 'dataframe':
+ dataIN = pd.read_csv(import_filepath)
else:
dataIN = import_filepath
+
+ if show_data is False:
+ plt.close()
+
return dataIN
@@ -4962,7 +5070,7 @@ Source code for sprit.sprit_hvsr
hvsr_out = hvsr_data
hvsr_out[site_name]['ProcessingStatus']['HVStatus']=False
hvsr_out[site_name]['ProcessingStatus']['OverallStatus'] = False
- hvsr_out = HVSRBatch(hvsr_out)
+ hvsr_out = HVSRBatch(hvsr_out, df_as_read=hvsr_data.input_df)
hvsr_out = _check_processing_status(hvsr_out, start_time=start_time, func_name=inspect.stack()[0][3], verbose=verbose)
return hvsr_out
@@ -5288,7 +5396,7 @@ Source code for sprit.sprit_hvsr
hvsr_out['processing_parameters'] = {}
hvsr_out['processing_parameters']['process_hvsr'] = {}
for key, value in orig_args.items():
- hvsr_out['processing_parameters']['generate_psds'][key] = value
+ hvsr_out['processing_parameters']['process_hvsr'][key] = value
if str(horizontal_method) == '8' or horizontal_method.lower() == 'single azimuth':
if azimuth is None:
@@ -5540,7 +5648,7 @@ Source code for sprit.sprit_hvsr
hvsr_data[site_name]['ProcessingStatus']['OverallStatus']=False
hvsr_out = hvsr_data
- output = HVSRBatch(hvsr_out)
+ output = HVSRBatch(hvsr_out, df_as_read=hvsr_data.input_df)
return output
if not isinstance(hvsr_data, (HVSRData, dict, obspy.Stream, obspy.Trace)):
@@ -5825,7 +5933,7 @@ Source code for sprit.sprit_hvsr
hvsr_out = hvsr_data
hvsr_out[site_name]['ProcessingStatus']['RemoveOutlierCurves'] = False
hvsr_out[site_name]['ProcessingStatus']['OverallStatus'] = False
- hvsr_out = HVSRBatch(hvsr_out)
+ hvsr_out = HVSRBatch(hvsr_out, df_as_read=hvsr_data.input_df)
hvsr_out = _check_processing_status(hvsr_out, start_time=start_time, func_name=inspect.stack()[0][3], verbose=verbose)
return hvsr_out
@@ -5985,6 +6093,125 @@ Source code for sprit.sprit_hvsr
+# Update all elevation-related attriutes
+
+[docs]
+def update_elevation(hvsr_data, updated_surface_elevation, updated_elevation_unit):
+ """Function to quickly update all attributes associated with elevation of an HVSRData object
+
+ Parameters
+ ----------
+ hvsr_data : HVSRData or HVSRBatch
+ HVSRData or HVSRBatch object containing attributes related to elevation.
+ If HVSRBatch, updated_surface_elevation should be list or tuple and
+ updated_elevation_unit may either be str or list/tuple of strings.
+ updated_surface_elevation : numbers.Number
+ Number (float or int) with the updated elevation.
+ Meters is the preferred unit. If feet are used instead, it will be converted to meters.
+ updated_elevation_unit : str
+ Unit used for updated_surface_elevation. If 'feet', it will be converted to meters.
+
+ Returns
+ -------
+ HVSRData
+ HVSRData object with all attributes related to elevation updated
+ """
+
+ # Break out for HVSRBatch
+ if isinstance(hvsr_data, HVSRBatch):
+ if len(updated_surface_elevation) != len(hvsr_data.sites):
+ warnings.warn(f'Elevations for HVSRBatch object could not be updated. \
+ Length of updated_surface_elevation ({len(updated_surface_elevation)}) must equal\
+ the number of sites ({len(hvsr_data.sites)}) in hvsr_data')
+ return hvsr_data
+
+ if isinstance(updated_elevation_unit, (list, tuple)):
+ if len(updated_elevation_unit) != len(hvsr_data.sites):
+ warnings.warn(f'Elevations for HVSRBatch object could not be updated. \
+ Length of updated_elevation_unit ({len(updated_elevation_unit)}) must equal\
+ the number of sites ({len(hvsr_data.sites)}) in hvsr_data')
+ return hvsr_data
+
+ elif type(updated_elevation_unit) is str:
+ updated_elevation_unit = [updated_elevation_unit] * len(hvsr_data.sites)
+ else:
+ warnings.warn(f"updated_elevation_unit must be list, tuple, or str, not {type(updated_elevation_unit)}")
+
+ for i, sitename in enumerate( hvsr_data):
+ hvsr_data[sitename] = update_elevation(hvsr_data[sitename],
+ updated_surface_elevation[i],
+ updated_elevation_unit[i])
+ return hvsr_data
+
+ #elevation_attrs = ['elevation', 'x_elev_m', 'x_elev_ft']
+ if hasattr(hvsr_data, 'elevation'):
+ elev_diff = hvsr_data['elevation'] - updated_surface_elevation
+ else:
+ elev_diff = -1 * updated_surface_elevation
+
+
+ mList = ['meters', 'm', 'standard', 'metric', 'si', 'metres', 'metre', 'meter']
+ fList = ['feet', 'ft', 'f', 'foot', 'american', 'imperial', 'imp']
+
+ # Update parameters with elevations in them
+ if str(updated_elevation_unit).lower() in fList:
+ updated_surface_elevation = updated_surface_elevation * 0.3048
+ hvsr_data['elevation'] = updated_surface_elevation
+
+ hvsr_data['elev_unit'] = 'meters'
+
+ if hasattr(hvsr_data, 'x_elev_m'):
+ hvsr_data['x_elev_m']['Z'] = hvsr_data['x_elev_m']['Z'] - elev_diff
+ hvsr_data['x_elev_m']['E'] = hvsr_data['x_elev_m']['E'] - elev_diff
+ hvsr_data['x_elev_m']['N'] = hvsr_data['x_elev_m']['N'] - elev_diff
+
+ hvsr_data['x_elev_ft']['Z'] = hvsr_data['x_elev_m']['Z'] / 0.3048
+ hvsr_data['x_elev_ft']['E'] = hvsr_data['x_elev_m']['E'] / 0.3048
+ hvsr_data['x_elev_ft']['N'] = hvsr_data['x_elev_m']['N'] / 0.3048
+
+ # Update elevations in Table_Report
+ table_report_cols = ['Elevation', 'BedrockElevation']
+ if hasattr(hvsr_data, 'Table_Report'):
+ hvsr_data.Table_Report['Elevation'] = updated_surface_elevation
+ if 'BedrockDepth' in hvsr_data.Table_Report.columns:
+ hvsr_data.Table_Report['BedrockElevation'] = updated_surface_elevation - hvsr_data.Table_Report['BedrockDepth']
+
+ # Update elevations in Print_Report
+ if hasattr(hvsr_data, "Print_Report"):
+ hvsr_data['Print_Report'] = re.sub(r"Elevation:\s*[\d.]+",
+ f"Elevation: {updated_surface_elevation}",
+ hvsr_data['Print_Report'])
+
+ # Update elevations in HTML_Report
+ if hasattr(hvsr_data, "HTML_Report"):
+ hvsr_data['HTML_Report'] = re.sub(r"Elevation:\s*[\d.]+",
+ f"Elevation: {updated_surface_elevation}",
+ hvsr_data['HTML_Report'])
+
+ # Update elevations in PeakReport attributes
+ azList = ['HV']
+ azList.extend(list(hvsr_data.hvsr_az.keys()))
+ for az in azList:
+ for peakReport in hvsr_data.PeakReport[az]:
+ if 'Table_Report' in peakReport['Report']: #This is a dict
+ peakReport['Report']['Table_Report']['Elevation'] = updated_surface_elevation
+ if 'BedrockDepth' in peakReport['Report']['Table_Report'].columns:
+ peakReport['Report']['Table_Report']['BedrockElevation'] = updated_surface_elevation - peakReport['Report']['Table_Report']['BedrockDepth']
+
+ if 'Print_Report' in peakReport['Report']: #This is a dict
+ peakReport['Report']['Print_Report'] = re.sub(r"Elevation:\s*[\d.]+",
+ f"Elevation: {updated_surface_elevation}",
+ peakReport['Report']['Print_Report'])
+
+ # Update processing_parameters to reflect new elevations
+ hvsr_data['processing_parameters']['fetch_data']['params']['elevation'] = updated_surface_elevation
+ hvsr_data['processing_parameters']['fetch_data']['params']['elev_unit'] = 'meters'
+ hvsr_data['processing_parameters']['fetch_data']['params']['params']['elevation'] = updated_surface_elevation
+ hvsr_data['processing_parameters']['fetch_data']['params']['params']['elev_unit'] = 'meters'
+
+ return hvsr_data
+
+
# BATCH FUNCTIONS: various functions that are used to help the regular functions handle batch data
# Helper function for batch processing of check_peaks
def __check_peaks_batch(**check_peaks_kwargs):
@@ -9205,8 +9432,8 @@ Source code for sprit.sprit_hvsr
# Annotate all peaks
if 'ann' in plot_type:
- for i, p in enumerate(hvsr_data['hvsr_peak_freqs']):
- y = hvsr_data['hvsr_curve'][hvsr_data['hvsr_peak_indices'][i]]
+ for i, p in enumerate(hvsr_data['hvsr_peak_freqs'][azimuth]):
+ y = hvsr_data['hvsr_curve'][hvsr_data['hvsr_peak_indices'][azimuth][i]]
ax.annotate('Peak at '+str(round(p,2))+'Hz', (p, 0.1), xycoords='data',
horizontalalignment='center', verticalalignment='bottom',
bbox=dict(facecolor='w', edgecolor='none', alpha=0.8, pad=0.1))
@@ -10050,7 +10277,7 @@ Source code for sprit.sprit_hvsr
# HELPER functions for checking peaks
# Initialize peaks
-def __init_peaks(_x, _y, _index_list, _hvsr_band, peak_freq_range=[0.4, 40], _min_peak_amp=1):
+def __init_peaks(_x, _y, _index_list, _hvsr_band, peak_freq_range=[0.4, 40], _min_peak_amp=0):
""" Initialize peaks.
Creates dictionary with relevant information and removes peaks in hvsr curve that are not relevant for data analysis (outside HVSR_band)
diff --git a/docs/_build/html/_modules/sprit/sprit_jupyter_UI.html b/docs/_build/html/_modules/sprit/sprit_jupyter_UI.html
index c755f2e..5fc873b 100644
--- a/docs/_build/html/_modules/sprit/sprit_jupyter_UI.html
+++ b/docs/_build/html/_modules/sprit/sprit_jupyter_UI.html
@@ -3,7 +3,7 @@
- sprit.sprit_jupyter_UI — sprit 2.0 documentation
+ sprit.sprit_jupyter_UI — sprit 2.1-dev documentation
@@ -12,7 +12,7 @@
-
+
diff --git a/docs/_build/html/_modules/sprit/sprit_plot.html b/docs/_build/html/_modules/sprit/sprit_plot.html
index a4f8cb1..3024c62 100644
--- a/docs/_build/html/_modules/sprit/sprit_plot.html
+++ b/docs/_build/html/_modules/sprit/sprit_plot.html
@@ -3,7 +3,7 @@
- sprit.sprit_plot — sprit 2.0 documentation
+ sprit.sprit_plot — sprit 2.1-dev documentation
@@ -12,7 +12,7 @@
-
+
@@ -73,6 +73,8 @@
Source code for sprit.sprit_plot
import datetime
import inspect
+import math
+import numbers
import os
import pathlib
import webbrowser
@@ -81,17 +83,21 @@ Source code for sprit.sprit_plot
import ipywidgets as widgets
from IPython.display import display, clear_output
+import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import plotly.express as px
import plotly.graph_objs as go
import plotly.subplots as subplots
-from scipy import signal
+from scipy import signal, interpolate
+import shapely
try:
import sprit_hvsr
+ import sprit_calibration
except:
import sprit.sprit_hvsr as sprit_hvsr
+ import sprit.sprit_calibration as sprit_calibration
[docs]
@@ -1269,6 +1275,561 @@ Source code for sprit.sprit_plot
return outlier_fig
+
+
+[docs]
+def plot_depth_curve(hvsr_results, use_elevation=True, show_feet=False, normalize_curve=True,
+ depth_limit=250, max_elev=None, min_elev=None,
+ annotate=True, depth_plot_export_path=None,
+ fig=None, ax=None, show_depth_curve=True):
+
+ if fig is None and ax is None:
+ fig, ax = plt.subplots(layout='constrained')
+ fig.set_size_inches(3, 5)
+ fig.suptitle(hvsr_results['site'])
+ ax.set_title('Calibrated Depth to Interface', size='small')
+ ax.tick_params(top=True, labeltop=True, bottom=False, labelbottom=False)
+
+ surfElev = hvsr_results.Table_Report['Elevation'][0]
+ bedrockElev = hvsr_results.Table_Report['BedrockElevation'][0]
+ bedrockDepth = hvsr_results.Table_Report['BedrockDepth'][0]
+ curveRange = max(hvsr_results.hvsr_curve) - min(hvsr_results.hvsr_curve)
+
+ if normalize_curve:
+ curvePlot = (hvsr_results.hvsr_curve - min(hvsr_results.hvsr_curve)) / curveRange
+ xBase = 0
+ xCap = 1
+ xLims = [-0.25, 1.25]
+ ax.set_xticks([0, 1])
+ else:
+ curvePlot = hvsr_results.hvsr_curve
+ xBase = min(hvsr_results.hvsr_curve)
+ xCap = max(hvsr_results.hvsr_curve)
+ xLims = [xBase-(0.15*curveRange), xCap+(0.15*curveRange)]
+
+ if use_elevation:
+ yLims = [hvsr_results.x_elev_m['Z'][0] - depth_limit,
+ hvsr_results.x_elev_m['Z'][0]]
+ yVals = hvsr_results.x_elev_m['Z'][:-1]
+ ax.set_ylabel('Elevation [m]')
+ bedrockVal = bedrockElev
+ if annotate:
+ #Annotate surface elevation
+ ax.text(x=xLims[0],
+ y=surfElev,
+ s=str(round(surfElev, 2))+'m',
+ ha='right',
+ va='bottom',
+ size='x-small')
+
+ # Annotate bedrock elevation
+ ax.text(x=xBase,
+ y=bedrockElev,
+ s=' ' + str(round(bedrockElev, 2))+'m\n elevation',
+ ha='left',
+ va='center',
+ size='x-small')
+
+ # Annotate bedrock depth
+ ax.text(x=xBase,
+ y=max(yLims),
+ s=str(round(bedrockDepth, 2))+'m deep ',
+ ha='right',
+ va='top',
+ size='x-small',
+ rotation='vertical')
+ else:
+ yLims = [depth_limit, hvsr_results.x_depth_m['Z'][0]]
+ yVals = hvsr_results.x_depth_m['Z'][:-1]
+ ax.set_ylabel('Depth [m]')
+ bedrockVal = bedrockDepth
+ if annotate:
+ # Annotate surface elevation
+ ax.text(x=xLims[0],
+ y=0,
+ s=str(round(surfElev, 2))+'m',
+ ha='right',
+ va='bottom',
+ size='x-small')
+
+ # Annotate Bedrock elevation
+ ax.text(x=xBase,
+ y=bedrockVal,
+ s=str(round(bedrockElev, 2))+'m\nelevation',
+ ha='center',
+ va='center',
+ size='x-small')
+
+ # Annotate Bedrock depth
+ ax.text(x=xBase,
+ y=(min(yLims)+bedrockDepth)/2,
+ s=str(round(bedrockDepth, 2))+'m deep',
+ ha='right',
+ va='top',
+ size='x-small',
+ rotation='vertical')
+
+ # Plot curve
+ ax.fill_betweenx(y=yVals, x1=xBase, x2=curvePlot, alpha=0.2, facecolor='k')
+ ax.plot(curvePlot, yVals, c='k', linewidth=0.5)
+ if show_feet:
+ ax_ft = ax.twinx()
+ ax_ft.plot(curvePlot, yVals*3.281, alpha=0)
+ ax_ft.set_ylim(yLims[0]*3.281, yLims[1]*3.281)
+ ax_ft.set_ylabel('Elevation [ft]')
+ if not use_elevation:
+ ax_ft.set_ylabel('Depth [ft]')
+
+ # Plot peak location
+ ax.hlines(y=bedrockVal,
+ xmin=xBase, xmax=xCap,
+ linestyles='dotted', colors='k', linewidths=0.5)
+ ax.scatter(xBase, y=bedrockVal, c='k', s=0.5)
+ ax.scatter(xCap, y=bedrockVal, c='k', s=0.5)
+
+ # Plot "base" line
+ ax.axvline(x=xBase, linestyle='dotted', c='k', linewidth=0.5)
+
+ ax.set_ylim(yLims)
+ ax.set_xlim(xLims)
+
+ xlabel = "H/V Ratio"
+ if normalize_curve:
+ xlabel += '\n(Normalized)'
+ ax.set_xlabel('H/V Ratio')
+ ax.xaxis.set_label_position('top')
+ ax.set_title(hvsr_results['site'])
+
+ plt.sca(ax)
+ if show_depth_curve:
+ plt.show()
+ else:
+ plt.close()
+
+ if depth_plot_export_path is not None:
+ if isinstance(depth_plot_export_path, os.PathLike):
+ fig.savefig(depth_plot_export_path)
+ else:
+ print(f'Please specify a valid path for depth_plot_export_path, not {depth_plot_export_path}')
+
+ hvsr_results['Depth_Plot'] = fig
+ return hvsr_results
+
+
+
+[docs]
+def plot_cross_section(hvsr_data, title=None, fig=None, ax=None, use_elevation=True, show_feet=False, primary_unit='m',
+ show_curves=True, annotate_curves=False, curve_alignment='peak',
+ grid_size='auto', orientation='WE', interpolation_type='cloughtocher',
+ surface_elevations=None, show_peak_points=True, smooth_bedrock_surface=False,
+ depth_limit=150, minimum_elevation=None, show_bedrock_surface=True,
+ return_data_batch=True, show_cross_section=True, verbose=False,
+ **kwargs):
+
+ if verbose:
+ print("Getting cross section plot configuration")
+
+ if fig is None and ax is None:
+ fig, ax = plt.subplots()
+ elif ax is None and fig is not None:
+ fig = fig
+ ax = fig.get_axes()[0]
+ elif fig is None and ax is not None:
+ ax = ax
+ fig = plt.figure()
+ fig.axes.append(ax)
+ else:
+ fig = fig
+ ax = ax
+ plt.sca(ax)
+
+ if verbose:
+ print("Getting data batch for cross section plot")
+ batchExt = None
+ if not isinstance(hvsr_data, sprit_hvsr.HVSRBatch) :
+ if pathlib.Path(hvsr_data).exists() and pathlib.Path(hvsr_data).is_dir():
+ batchExt = 'hvsr'
+ hvDataBatch = sprit_hvsr.HVSRBatch(hvsr_data, batch_ext=batchExt)
+
+ if verbose:
+ print("Sorting and Orienting data")
+ # Get orientation/order of data
+ nsList = ['ns', "north-south", 'northsouth', 'south', 's']
+ snList = ['sn', "south-north", 'southnorth', 'north', 'n']
+ weList = ['we', "west-east", 'westeast', 'east', 'e']
+ ewList = ['ew', "east-west", 'eastwest', 'west', 'w']
+
+ if str(orientation).lower() in nsList:
+ ordercoord = 'latitude'
+ order = 'descending'
+ profile_direction = 'north-south'
+ elif str(orientation).lower() in snList:
+ ordercoord = 'latitude'
+ order = 'ascending'
+ profile_direction = 'south-north'
+ elif str(orientation).lower() in weList:
+ ordercoord = 'longitude'
+ order = 'ascending'
+ profile_direction = 'west-east'
+ elif str(orientation).lower() in ewList:
+ ordercoord = 'longitude'
+ order = 'descending'
+ profile_direction = 'east-west'
+ else:
+ if verbose:
+ print(f"Value for orientation={orientation} is not recognized. Using West-East orientation.")
+ order = 'ascending'
+ ordercoord='longitude'
+ profile_direction = 'west-east (default)'
+
+ # Get data in correct order, as specified by orientation parameter
+ reverseit = (order == 'descending')
+ sorted_sites = sorted(hvDataBatch, key=lambda site: hvDataBatch[site][ordercoord], reverse=reverseit)
+ hvDataSorted = [hvDataBatch[h] for h in sorted_sites]
+
+ if verbose:
+ print(f'Plotting {len(hvDataBatch.sites)} sites, {profile_direction}.')
+ [print(f"\t{hvdata.site[:12]:<12}: {hvdata.longitude:>8.4f}, {hvdata.latitude:>8.4f}, {hvdata.elevation:<6.1f}") for hvdata in hvDataSorted]
+
+ # Get cross section profile
+ shapelyPoints = []
+ interpData = []
+ interpCoords = {'longitude':[], 'latitude':[], 'elevation':[]}
+ for i, hvData in enumerate(hvDataSorted):
+ if not hasattr(hvData, 'x_elev_m'):
+ calc_depth_kwargs = {k: v for k, v in kwargs.items() if k in tuple(inspect.signature(sprit_calibration.calculate_depth).parameters.keys())}
+ hvData = sprit_calibration.calculate_depth(hvData, **calc_depth_kwargs, verbose=verbose)
+
+ #print(hvData['longitude'], hvData['latitude'])
+ # Create shapely Point objects at each profile location
+ x = hvData['longitude']
+ y = hvData['latitude']
+ z = hvData['elevation']
+
+ shapelyPoints.append(shapely.Point(x, y, z))
+
+ #Points arranged for interpolation
+ interpData.extend(list(hvData.hvsr_curve))
+ for i, pt in enumerate(hvData.hvsr_curve):
+ interpCoords['longitude'].append(x)
+ interpCoords['latitude'].append(y)
+ interpCoords['elevation'].append(hvData['x_elev_m']['Z'][i])
+
+ #Since already doing loop, ensure hvData has all depth/elev info it needs
+ if not hasattr(hvData, 'x_elev_m'):
+ calc_depth_kwargs = {k: v for k, v in kwargs.items()
+ if k in tuple(inspect.signature(sprit_calibration.calculate_depth).parameters.keys())}
+ if 'calculate_depth_in_feet' not in calc_depth_kwargs:
+ calc_depth_kwargs['calculate_depth_in_feet'] = True
+ hvDataSorted[i] = sprit_calibration.calculate_depth(hvData, **calc_depth_kwargs, verbose=verbose)
+
+ xSectionProfile = shapely.LineString(shapelyPoints)
+ profileXs, profileYs = xSectionProfile.xy
+
+ orderCoordValues = profileXs
+ if ordercoord == 'latitude':
+ orderCoordValues = profileYs
+
+ minX = min(profileXs)
+ minY = min(profileYs)
+ maxX = max(profileXs)
+ maxY = max(profileYs)
+
+ # Generate grid
+ if verbose:
+ print("Generating Grid: ", end='')
+ xSectionLength = xSectionProfile.length
+ if grid_size == 'auto':
+ grid_size=(50, 100)
+
+ cellHNumber = grid_size[0]
+ cellWNumber = grid_size[1]
+
+ elif isinstance(grid_size, (list, tuple)):
+ cellHNumber = grid_size[0]
+ cellWNumber = grid_size[1]
+ else:
+ grid_size=(50, 100)
+
+ cellHNumber = grid_size[0]
+ cellWNumber = xSectionLength/grid_size[1]
+
+ if verbose:
+ print(f'grid_size value ({grid_size} not recognized, using grid 100 cells wide and 50 cells high: grid_size=(50, 100))')
+
+ cellWSize = xSectionLength/cellWNumber
+
+ max_surf_elev = max([hvd.elevation for hvd in hvDataSorted])
+ min_br_elev = min([hvd.Table_Report['Peak'][0] for hvd in hvDataSorted])
+ elev_range = max_surf_elev - min_br_elev
+
+ max_grid_elev = math.ceil(max_surf_elev)
+
+ # Minimum grid elevation is determined by depth_limit and minimum_elevation
+ if str(minimum_elevation).lower() == 'auto':
+ min_grid_elev = min_br_elev - (elev_range) * 0.1
+ elif isinstance(minimum_elevation, numbers.Number):
+ min_grid_elev = minimum_elevation
+ elif minimum_elevation is None:
+ min_grid_elev = max_grid_elev - depth_limit
+
+ xSectionDepth = max_grid_elev - min_grid_elev
+ cellHSize = xSectionDepth/cellHNumber
+
+ # Get grid coordinates (all coords in z direction (depth/elev))
+ gridZcoords = np.linspace(min_grid_elev, max_grid_elev, cellHNumber)
+
+ gridXDists = np.linspace(0, xSectionProfile.length, cellWNumber)
+ gridXcoords = [] # All coords in the "x" direction (along profile)
+ for xdist in gridXDists:
+ x, y = xSectionProfile.interpolate(xdist).xy
+ if 'east' in profile_direction:
+ gridXcoords.append(x[0])
+ else:
+ gridXcoords.append(y[0])
+ gridXcoords = np.array(gridXcoords)
+ if verbose:
+ print(f'Grid generated ({cellWNumber*cellHNumber} cells)\n\tx-range: {xSectionLength:.5f} ({cellWNumber:d} cells, each {cellWSize:.5f} units in size)\n\tz-range: {xSectionDepth:.2f} ({cellHNumber:d} cells, each {cellHSize:.5f} units in size)')
+
+ #print('x', len(interpCoords['longitude']))
+ #print('y', len(interpCoords['latitude']))
+ #print('z', len(interpCoords['elevation']))
+ #print('interp', np.array(interpData).shape)
+ if verbose:
+ print(f'Beginning interpolation ({interpolation_type})... ', end='')
+
+ ctList = ['cloughtocher2dinterpolator', 'cloughtocher', 'ct', 'clough-tocher', 'clough tocher', 'cubic', 'c']
+ nearList = ['nearestnd', 'nearest', 'near', 'n']
+ linList = ['linearnd', 'linear', 'lin', 'l']
+ rbfList = ['radial basis function', 'rbf', 'rbfinterpolator']
+
+ if str(interpolation_type).lower() in ctList:
+ interp = interpolate.CloughTocher2DInterpolator(list(zip(interpCoords[ordercoord], interpCoords['elevation'])), interpData)
+ elif str(interpolation_type).lower() in nearList:
+ interp = interpolate.NearestNDInterpolator(list(zip(interpCoords[ordercoord], interpCoords['elevation'])), interpData)
+ elif str(interpolation_type).lower() in rbfList:
+ interp = interpolate.RBFInterpolator(list(zip(interpCoords[ordercoord], interpCoords['elevation'])), interpData)
+ elif str(interpolation_type).lower() in linList:
+ interp = interpolate.LinearNDInterpolator(list(zip(interpCoords[ordercoord], interpCoords['elevation'])), interpData)
+
+ xx, zz = np.meshgrid(gridXcoords, gridZcoords)
+ interpData = interp(xx, zz)
+ interpDataflat = interpData[:-1, :-1]
+ if verbose:
+ print('Data interpolated')
+ print('Plotting colormesh')
+
+
+ # kwargs-defined pcolormesh kwargs
+ pcolormeshKwargs = {k: v for k, v in kwargs.items() if k in tuple(inspect.signature(plt.pcolormesh).parameters.keys())}
+
+ # Set defaults for cmap and shading (if not overriden in kwargs)
+ if 'cmap' not in pcolormeshKwargs:
+ pcolormeshKwargs['cmap'] = 'nipy_spectral'
+ if 'shading' not in pcolormeshKwargs:
+ pcolormeshKwargs['shading'] = 'flat'
+
+ ax.pcolormesh(xx, zz, interpDataflat, zorder=0, **pcolormeshKwargs)
+
+ if show_curves:
+ if verbose:
+ print('Plotting curves')
+ norm_div = 1
+ normal_factor = np.diff(orderCoordValues)
+ normal_factor = np.nanmedian(normal_factor[normal_factor != 0]) / norm_div
+
+ zAttr = 'x_depth_m'
+ if use_elevation:
+ zAttr = 'x_elev_m'
+
+ for hvData in hvDataSorted:
+ hvData['Normalized_HVCurve'] = (hvData['hvsr_curve'] / np.nanmax(hvData['hvsr_curve'])) * normal_factor
+ locatedCurve = hvData['Normalized_HVCurve'] + hvData[ordercoord]
+ if curve_alignment.lower() == 'peak':
+ normal_peak_factor = (hvData["BestPeak"]['HV']['A0'] / np.nanmax(hvData['hvsr_curve'])) * normal_factor
+ locatedCurve = locatedCurve - normal_peak_factor
+ elif curve_alignment.lower() == 'max':
+ locatedCurve = locatedCurve - normal_factor
+
+ if max(locatedCurve) > max(gridXcoords):
+ locatedCurve = locatedCurve - (max(locatedCurve) - max(gridXcoords))
+ if min(locatedCurve) < min(gridXcoords):
+ locatedCurve = locatedCurve + (min(gridXcoords) - min(locatedCurve))
+
+ ax.plot(locatedCurve, hvData[zAttr]['Z'][:-1], c='k', linewidth=0.5, zorder=3)
+
+ if annotate_curves:
+ for hvData in hvDataSorted:
+ if len(hvData.site) > 10:
+ sitename = hvData.site[:8]+ '...'
+ else:
+ sitename = hvData.site
+ ax.text(hvData[ordercoord], y=min_grid_elev, s=sitename, ha='right', va='bottom', rotation='vertical')
+
+ if smooth_bedrock_surface:
+ show_bedrock_surface = True
+
+ if show_peak_points or show_bedrock_surface:
+ brX = []
+ brZ = []
+ for hvData in hvDataSorted:
+ if 'BedrockElevation' in hvData['Table_Report'].columns:
+ brX.append(hvData[ordercoord])
+ brZ.append(hvData['Table_Report'].loc[0,'BedrockElevation'][()])
+ if show_peak_points:
+ ax.scatter(brX, brZ, zorder=5, c='k', marker='v')
+
+
+ if smooth_bedrock_surface:
+ #brSurfZ = scipy.signal.savgol(brZ, window_length=len(brZ))
+ if brX[0] > brX[-1]:
+ brX = np.flip(brX)
+ brZ = np.flip(brZ)
+ doFlip=True
+ else:
+ doFlip=False
+
+ newX = np.sort(gridXcoords)
+ brSurfZ = np.interp(newX, brX, brZ)
+ brSurfX = newX
+ else:
+ brSurfX = brX
+ brSurfZ = brZ
+
+ zMinPts = list(np.array(brSurfZ) * 0 + min(gridZcoords))
+
+ if show_bedrock_surface:
+ ax.fill_between(brSurfX, brSurfZ, zMinPts,facecolor='w', alpha=0.5, zorder=1)
+ ax.plot(brSurfX, brSurfZ, c='k', zorder=2)
+
+
+ # Plot surfaces
+ if verbose:
+ print('Plotting surfaces')
+ if surface_elevations is None:
+ surfPts_shapely = []
+ surfPtsX = []
+ surfPtsZ = []
+
+ surface_elevations = shapely.LineString([shapely.Point(hvData['longitude'],
+ hvData["latitude"],
+ hvData["elevation"])
+ for hvData in hvDataSorted])
+
+ xPts = []
+ zPts = []
+ for surf_pt in surface_elevations.coords:
+ surfPtDict = {'longitude':surf_pt[0],
+ 'latitude': surf_pt[1],
+ 'elevation': surf_pt[2]}
+ xPts.append(surfPtDict[ordercoord])
+ zPts.append(surfPtDict['elevation'])
+
+ zMaxPts = list(np.array(zPts) * 0 + max_grid_elev)
+ ax.fill_between(xPts, zPts, zMaxPts, facecolor='w', zorder=1000)
+ ax.plot(xPts, zPts, c='g', linewidth=1.5, zorder=1001)
+
+ # Plot configuration
+ if verbose:
+ print('Configuring plot')
+ ax.set_xlim([min(gridXcoords), max(gridXcoords)])
+ ax.set_ylim([min_grid_elev, max_grid_elev])
+
+
+ ax.tick_params(top=True, labeltop=True, bottom=False, labelbottom=False)
+ ax.set_xlabel(str(ordercoord).title())
+ ax.xaxis.set_label_position('top')
+ ax.set_ylabel('Elevation [Meters]')
+ if title is None:
+ title = 'HVSR Cross Section Profile'
+ ax.set_title(title)
+
+ # Calculate angle
+ profile_angle = math.degrees(math.atan2(shapelyPoints[-1].y - shapelyPoints[0].y, shapelyPoints[-1].x - shapelyPoints[0].x))
+ #Convert angle to geographic coordinates
+ profile_angle = (profile_angle*-1) + 90
+ if profile_angle < 0:
+ profile_angle += 360
+
+ if verbose:
+ print(f"Calculated profile angle to be {profile_angle:.3f} degrees.")
+ # Calculate nomencalture
+ if profile_angle < -11.25 + 22.5 * 1:
+ profileStart = 'S'
+ profileEnd = 'N'
+ elif profile_angle < -11.25 + 22.5 * 2:
+ profileEnd = 'NNE'
+ profileStart = 'SSW'
+ elif profile_angle < -11.25 + 22.5 * 3:
+ profileEnd = 'NE'
+ profileStart = 'SW'
+ elif profile_angle < -11.25 + 22.5 * 4:
+ profileEnd = 'ENE'
+ profileStart = 'WSW'
+ elif profile_angle < -11.25 + 22.5 * 5:
+ profileEnd = 'E'
+ profileStart = 'W'
+ elif profile_angle < -11.25 + 22.5 * 6:
+ profileEnd = 'ESE'
+ profileStart = 'WNW'
+ elif profile_angle < -11.25 + 22.5 * 7:
+ profileEnd = 'SE'
+ profileStart = 'NW'
+ elif profile_angle < -11.25 + 22.5 * 8:
+ profileEnd = 'SSE'
+ profileStart = 'NNW'
+ elif profile_angle < -11.25 + 22.5 * 9:
+ profileEnd = 'S'
+ profileStart = 'N'
+ elif profile_angle < -11.25 + 22.5 * 10:
+ profileEnd = 'SSW'
+ profileStart = 'NNE'
+ elif profile_angle < -11.25 + 22.5 * 11:
+ profileEnd = 'SW'
+ profileStart = 'NE'
+ elif profile_angle < -11.25 + 22.5 * 12:
+ profileEnd = 'WSW'
+ profileStart = 'ENE'
+ elif profile_angle < -11.25 + 22.5 * 13:
+ profileEnd = 'W'
+ profileStart = 'E'
+ elif profile_angle < -11.25 + 22.5 * 14:
+ profileEnd = 'WNW'
+ profileStart = 'ESE'
+ elif profile_angle < -11.25 + 22.5 * 15:
+ profileEnd = 'NW'
+ profileStart = 'SE'
+ elif profile_angle < -11.25 + 22.5 * 16:
+ profileEnd = 'NNW'
+ profileStart = 'SSE'
+ elif profile_angle <= 360:
+ profileEnd = 'N'
+ profileStart = 'S'
+
+ if 'north' in profile_direction[:5] or 'east' in profile_direction[:5]:
+ ax.invert_xaxis()
+ #print('inverting')
+ #profileInt = profileEnd
+ #profileEnd = profileStart
+ #profileStart = profileInt
+
+ plt.sca(ax)
+ plt.figtext(0.1,0.95, s=profileStart)
+ plt.figtext(0.9,0.95, s=profileEnd)
+
+ if show_cross_section:
+ if verbose:
+ print('Displaying plot')
+ plt.sca(ax)
+ plt.show()
+
+ if return_data_batch:
+ hvBatch = sprit_hvsr.HVSRBatch(hvDataSorted)
+ hvBatch['Cross_Section_Plot'] = fig
+ return hvBatch
+
+ return fig
+
diff --git a/docs/_build/html/_modules/sprit/sprit_streamlit_ui.html b/docs/_build/html/_modules/sprit/sprit_streamlit_ui.html
new file mode 100644
index 0000000..eca7671
--- /dev/null
+++ b/docs/_build/html/_modules/sprit/sprit_streamlit_ui.html
@@ -0,0 +1,694 @@
+
+
+
+
+
+ sprit.sprit_streamlit_ui — sprit 2.1-dev documentation
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Source code for sprit.sprit_streamlit_ui
+import datetime
+import inspect
+import pathlib
+import sys
+import tempfile
+import zoneinfo
+
+import numpy as np
+import streamlit as st
+from obspy import UTCDateTime
+from obspy.signal.spectral_estimation import PPSD
+
+try:
+ from sprit import sprit_hvsr
+except Exception:
+ try:
+ import sprit_hvsr
+ except Exception:
+ import sprit
+
+verbose = False
+
+if verbose:
+ print('Start of file, session state length: ', len(st.session_state.keys()))
+param2print = None# 'period_limits'
+
+[docs]
+def print_param(key=param2print, show_type=True):
+ if key is None:
+ pass
+ elif key in st.session_state.keys():
+ print(key, st.session_state[key], 'type:', type(st.session_state[key]))
+
+print_param(param2print)
+
+icon=r"C:\Users\riley\LocalData\Github\SPRIT-HVSR\sprit\resources\icon\sprit_icon_alpha.ico"
+icon=":material/ssid_chart:"
+aboutStr = """
+# About SpRIT
+## v1.0.2
+
+SpRIT is developed by Riley Balikian at the Illinois State Geological Survey.
+
+Please visit the following links for any questions:
+* [API Documentation](https://sprit.readthedocs.io/en/latest/)
+* [Wiki](https://github.com/RJbalikian/SPRIT-HVSR/wiki)
+* [Pypi Repository](https://pypi.org/project/sprit/)
+
+"""
+if verbose:
+ print('Start setting up page config, session state length: ', len(st.session_state.keys()))
+st.set_page_config('SpRIT HVSR',
+ page_icon=icon,
+ layout='wide',
+ menu_items={'Get help': 'https://github.com/RJbalikian/SPRIT-HVSR/wiki',
+ 'Report a bug': "https://github.com/RJbalikian/SPRIT-HVSR/issues",
+ 'About': aboutStr})
+
+if verbose:
+ print('Start setting up constants/variables, session state length: ', len(st.session_state.keys()))
+OBSPYFORMATS = ['AH', 'ALSEP_PSE', 'ALSEP_WTH', 'ALSEP_WTN', 'CSS', 'DMX', 'GCF', 'GSE1', 'GSE2', 'KINEMETRICS_EVT', 'KNET', 'MSEED', 'NNSA_KB_CORE', 'PDAS', 'PICKLE', 'Q', 'REFTEK130', 'RG16', 'SAC', 'SACXY', 'SEG2', 'SEGY', 'SEISAN', 'SH_ASC', 'SLIST', 'SU', 'TSPAIR', 'WAV', 'WIN', 'Y']
+bandVals=[0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1,2,3,4,5,6,7,8,9,10,20,30,40,50,60,70,80,90,100]
+
+# SETUP KWARGS
+if verbose:
+ print('Start setting up kwargs dicts, session state length: ', len(st.session_state.keys()))
+
+ip_kwargs = {}
+fd_kwargs = {}
+ca_kwargs = {}
+rn_kwargs = {}
+gppsd_kwargs = {}
+phvsr_kwargs = {}
+roc_kwargs = {}
+cp_kwargs = {}
+gr_kwargs = {}
+run_kwargs = {}
+
+if verbose:
+ print('Start getting default values, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+# Get default values
+sigList = [[sprit_hvsr.input_params, ip_kwargs], [sprit_hvsr.fetch_data, fd_kwargs], [sprit_hvsr.calculate_azimuth, ca_kwargs],
+ [sprit_hvsr.remove_noise, rn_kwargs], [sprit_hvsr.generate_psds, gppsd_kwargs], [PPSD, gppsd_kwargs],
+ [sprit_hvsr.process_hvsr, phvsr_kwargs], [sprit_hvsr.remove_outlier_curves, roc_kwargs],
+ [sprit_hvsr.check_peaks, cp_kwargs], [sprit_hvsr.get_report, gr_kwargs]]
+
+
+
+[docs]
+def setup_session_state():
+ if "default_params" not in st.session_state.keys():
+ # "Splash screen" (only shows at initial startup)
+ mainContainerInitText = """
+ # SpRIT HVSR
+ ## About
+ SpRIT HVSR is developed by the Illinois State Geological Survey, part of the Prairie Research Institute at the University of Illinois.
+
+ ## Links
+ * API Documentation may be accessed [here (hosted by ReadtheDocs)](https://sprit.readthedocs.io/en/latest/) and [here (hosted by Github Pages)](https://rjbalikian.github.io/SPRIT-HVSR/main.html)
+ * The Wiki and Tutorials may be accessed [here](https://github.com/RJbalikian/SPRIT-HVSR/wiki)
+ * Source Code may be accessed here: [https://github.com/RJbalikian/SPRIT-HVSR](https://github.com/RJbalikian/SPRIT-HVSR)
+ * PyPI repository may be accessed [here](https://pypi.org/project/sprit/)
+
+ ## MIT License
+ It is licensed under the MIT License:
+ > Permission is hereby granted, free of charge, to any person obtaining a copy
+ > of this software and associated documentation files (the "Software"), to deal
+ > in the Software without restriction, including without limitation the rights
+ > to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ > copies of the Software, and to permit persons to whom the Software is
+ > furnished to do so, subject to the following conditions:
+ >
+ > The above copyright notice and this permission notice shall be included in all
+ > copies or substantial portions of the Software.
+ >
+ > THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ > SOFTWARE.
+ """
+ st.markdown(mainContainerInitText, unsafe_allow_html=True)
+ if verbose:
+ print('Start sig loop, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+ for sig in sigList:
+ funSig = inspect.signature(sig[0])
+ for arg in funSig.parameters.keys():
+ if not (funSig.parameters[arg].default is funSig.parameters[arg].empty):
+ sig[1][arg] = funSig.parameters[arg].default
+ run_kwargs[arg] = funSig.parameters[arg].default
+
+ gppsd_kwargs['ppsd_length'] = run_kwargs['ppsd_length'] = 30
+ gppsd_kwargs['skip_on_gaps'] = run_kwargs['skip_on_gaps'] = True
+ gppsd_kwargs['period_step_octaves'] = run_kwargs['period_step_octaves'] = 0.03125
+ gppsd_kwargs['period_limits'] = run_kwargs['period_limits'] = [1/run_kwargs['hvsr_band'][1], 1/run_kwargs['hvsr_band'][0]]
+ if verbose:
+ print('Done getting kwargs: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+ print('Setting up session state: ', len(st.session_state.keys()))
+ #st.session_state["updated_kwargs"] = {}
+ for key, value in run_kwargs.items():
+ if verbose:
+ print(f'Resetting {key} to {value}')
+ print_param(param2print)
+
+ # if key in st.session_state.keys() and (st.session_state[key] != value):
+ st.session_state[key] = value
+
+ #listItems = ['source', 'tzone', 'elev_unit', 'data_export_format', 'detrend', 'special_handling', 'peak_selection', 'freq_smooth', 'horizontal_method', 'stalta_thresh']
+ ## Convert items to lists
+ #for arg, value in st.session_state.items():
+ # if arg in listItems:
+ # valList = [value]
+ # st.session_state[arg] = valList
+ # run_kwargs[arg] = st.session_state[arg]
+
+ strItems = ['channels', 'xcoord', 'ycoord', 'elevation', 'detrend_options', 'horizontal_method']
+ # Convert lists and numbers to strings
+ for arg, value in st.session_state.items():
+ if arg in strItems:
+ if isinstance(value, (list, tuple)):
+ newVal = '['
+ for item in value:
+ newVal = newVal+item+', '
+ newVal = newVal[:-2]+']'
+
+ st.session_state[arg] = newVal
+ run_kwargs[arg] = newVal
+ else:
+ st.session_state[arg] = str(value)
+ run_kwargs[arg] = str(value)
+
+ if verbose:
+ print_param(param2print)
+
+ dtimeItems = ['acq_date', 'starttime', 'endtime']
+ # Convert everything to python datetime objects
+ for arg, value in st.session_state.items():
+ if arg in dtimeItems:
+ if isinstance(value, str):
+ st.session_state[arg] = datetime.datetime.strptime(value, "%Y-%m-%d")
+ run_kwargs[arg] = datetime.datetime.strptime(value, "%Y-%m-%d")
+ elif isinstance(st.session_state[arg], UTCDateTime):
+ st.session_state[arg] = value.datetime
+ run_kwargs[arg] = value.datetime
+ else:
+ st.session_state[arg] = value
+ run_kwargs[arg] = value
+
+ if verbose:
+ print_param(param2print)
+
+ # Case matching
+ # Add if-statement for docs building
+ if len(st.session_state.keys()) > 0: #print('allkeys', list(st.session_state.keys()))
+ st.session_state.data_export_format = run_kwargs['data_export_format'] = st.session_state.data_export_format.upper()
+ st.session_state.detrend = run_kwargs['detrend'] = st.session_state.detrend.title()
+ st.session_state.remove_method = run_kwargs['remove_method'] = str(st.session_state.remove_method).title()
+ st.session_state.peak_selection = run_kwargs['peak_selection'] = st.session_state.peak_selection.title()
+ st.session_state.freq_smooth = run_kwargs['freq_smooth'] = st.session_state.freq_smooth.title()
+ st.session_state.source = run_kwargs['source'] = st.session_state.source.title()
+
+ if verbose:
+ print_param(param2print)
+
+
+ # Default adjustments
+ methodDict = {'None':'Geometric Mean', '0':'Diffuse Field Assumption', '1':'Arithmetic Mean', '2':'Geometric Mean', '3':'Vector Summation', '4':'Quadratic Mean', '5':'Maximum Horizontal Value', '6':'Azimuth'}
+ st.session_state.horizontal_method = run_kwargs['horizontal_method'] = methodDict[st.session_state.horizontal_method]
+ st.session_state.plot_engine = run_kwargs['plot_engine'] = 'Plotly'
+ if verbose:
+ print_param(param2print)
+
+
+ st.session_state.default_params = run_kwargs
+ st.session_state.run_kws = list(run_kwargs.keys())
+
+ if verbose:
+ for key, value in st.session_state.items():
+ print("session st: ", st.session_state[key], type( st.session_state[key]), '| rkwargs:', value, type(value))
+
+
+ if verbose:
+ print('Done with setup, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+
+setup_session_state()
+
+
+[docs]
+def check_if_default():
+ if len(st.session_state.keys()) > 0:
+ print('Checking defaults, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+if verbose:
+ check_if_default()
+
+
+[docs]
+def text_change(verbose=verbose):
+ #Just a function to run so something is done when text changes
+ if verbose:
+ print('TEXTCHange')
+
+
+
+[docs]
+def on_file_upload():
+ file = st.session_state.datapath_uploader
+ temp_dir = tempfile.mkdtemp()
+ path = pathlib.Path(temp_dir).joinpath(file.name)
+ with open(path, "wb") as f:
+ f.write(file.getvalue())
+ if verbose:
+ print(file.name)
+ st.session_state.input_data = path.as_posix()
+
+
+
+
+[docs]
+def on_run_data():
+ mainContainer = st.container()
+ inputTab, outlierTab, infoTab, resultsTab = mainContainer.tabs(['Data', 'Outliers', 'Info','Results'])
+ plotReportTab, csvReportTab, strReportTab = resultsTab.tabs(['Plot', 'Results Table', 'Print Report'])
+
+ if st.session_state.input_data!='':
+ srun = {}
+ for key, value in st.session_state.items():
+ if key in st.session_state.run_kws and value != st.session_state.default_params[key]:
+ srun[key] = value
+ # Get plots all right
+ srun['plot_engine'] = 'plotly'
+ srun['plot_input_stream'] = True
+ srun['show_plot'] = False
+ srun['verbose'] = False #True
+ if verbose:
+ print('SPRIT RUN', srun)
+ st.toast('Data is processing', icon="⌛")
+ with mainContainer:
+ spinnerText = 'Data is processing with default parameters.'
+ excludedKeys = ['plot_engine', 'plot_input_stream', 'show_plot', 'verbose']
+ NOWTIME = datetime.datetime.now()
+ secondaryDefaults = {'acq_date':datetime.date(NOWTIME.year, NOWTIME.month, NOWTIME.day),
+ 'hvsr_band':(0.4, 40), 'use_hv_curve':True,
+ 'starttime':datetime.time(0,0,0),
+ 'endtime':datetime.time(23,59,0),
+ 'peak_freq_range':(0.4, 40),
+ 'stalta_thresh':(8, 16),
+ 'period_limits':(0.025, 2.5),
+ 'remove_method':['Auto'],
+ 'elev_unit':'m',
+ 'plot_type':'HVSR p ann C+ p ann Spec p'
+ }
+ nonDefaultParams = False
+ for key, value in srun.items():
+ if key not in excludedKeys:
+ if key in secondaryDefaults and secondaryDefaults[key] == value:
+ pass
+ else:
+ nonDefaultParams = True
+ spinnerText = spinnerText + f"\n-\t {key} = {value} ({type(value)} is not {st.session_state.default_params[key]}; {type(st.session_state.default_params[key])})"
+ if nonDefaultParams:
+ spinnerText = spinnerText.replace('default', 'the following non-default')
+ with st.spinner(spinnerText):
+ st.session_state.hvsr_data = sprit_hvsr.run(input_data=st.session_state.input_data, **srun)
+
+ write_to_info_tab(infoTab)
+ st.balloons()
+
+ inputTab.plotly_chart(st.session_state.hvsr_data['InputPlot'], use_container_width=True)
+ outlierTab.plotly_chart(st.session_state.hvsr_data['OutlierPlot'], use_container_width=True)
+ plotReportTab.plotly_chart(st.session_state.hvsr_data['HV_Plot'], use_container_width=True)
+ csvReportTab.dataframe(data=st.session_state.hvsr_data['CSV_Report'])
+ strReportTab.text(st.session_state.hvsr_data['Print_Report'])
+
+ st.session_state.prev_datapath=st.session_state.input_data
+
+
+
+[docs]
+def write_to_info_tab(info_tab):
+ with info_tab:
+ st.markdown("# Processing Parameters Used")
+ for fun, kwargDict in sigList:
+ funSig = inspect.signature(fun)
+ #excludeKeys = ['params', 'hvsr_data', 'hvsr_results']
+ funMD = ""
+ for arg in funSig.parameters.keys():
+ if arg in st.session_state.keys():
+ funMD = funMD + f"""\n * {arg} = {st.session_state[arg]}"""
+
+ with st.expander(f"{fun.__name__}"):
+ st.write(funMD, unsafe_allow_html=True)
+
+
+
+# DEFINE SIDEBAR
+if verbose:
+ print('About to start setting up sidebar, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+with st.sidebar:
+ if verbose:
+ print('Start setting up sidebar, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+ st.header('SpRIT HVSR', divider='rainbow')
+ datapathInput = st.text_input("Datapath", key='input_data', placeholder='Enter data filepath (to be read by obspy.core.Stream.read())')
+ # st.file_uploader('Upload data file(s)', type=OBSPYFORMATS, accept_multiple_files=True, key='datapath_uploader', on_change=on_file_upload)
+ with st.expander("Click to access data uploader"):
+ st.file_uploader("Upload data file(s)", type=OBSPYFORMATS, accept_multiple_files=False, key='datapath_uploader', on_change=on_file_upload)
+
+ bottom_container = st.container()
+
+ # Create top menu
+ with bottom_container:
+
+ resetCol, readCol, runCol = st.columns([0.3, 0.3, 0.4])
+ resetCol.button('Reset', disabled=True, use_container_width=True)
+ readCol.button('Read', use_container_width=True, args=((True, )))
+ runCol.button('Run', type='primary', use_container_width=True, on_click=on_run_data)
+
+ if verbose:
+ print('Done setting up bottom container, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+ # Add if-statement for docs building
+ if len(list(st.session_state.keys())) > 0:
+ st.header('Settings', divider='gray')
+ with st.expander('Expand to modify settings'):
+ if verbose:
+ print('Setting up sidebar expander, session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+
+ ipSetTab, fdSetTab, rmnocSetTab, gpSetTab, phvsrSetTab, plotSetTab = st.tabs(['Input', 'Data', "Noise", 'PPSDs', 'H/V', 'Plot'])
+ #@st.experimental_dialog("Update Input Parameters", width='large')
+ #def open_ip_dialog():
+ with ipSetTab:
+ if verbose:
+ print('Setting up input tab, session state length: ', len(st.session_state.keys()))
+ st.text_input("Site Name", placeholder='HVSR Site', on_change=text_change, key='site')
+
+ #with st.expander('Primary Input Parameters', expanded=True):
+
+ st.text_input('Instrument', help='Raspberry Shake and Tromino are currently the only values with special treatment. If a filepath, can use a .inst instrument file (json format)', key='instrument')
+ st.text_input('Metadata Filepath', help='Filepath to instrument response file', key='metapath')
+
+ st.select_slider('HVSR Band', value=st.session_state.hvsr_band, options=bandVals, key='hvsr_band')
+ st.select_slider('Peak Frequency Range', value=st.session_state.peak_freq_range, options=bandVals, key='peak_freq_range')
+
+ # with st.expander('Acquisition Date/Time'):
+ st.date_input('Acquisition Date', format='YYYY-MM-DD', key='acq_date')
+ st.time_input('Start time', step=60, key='starttime')
+ st.time_input('End time', step=60, key='endtime')
+
+ tZoneList=list(zoneinfo.available_timezones())
+ tZoneList.sort()
+ tZoneList.insert(0, "localtime")
+ tZoneList.insert(0, "US/Pacific")
+ tZoneList.insert(0, "US/Eastern")
+ tZoneList.insert(0, "US/Central")
+ tZoneList.insert(0, "UTC")
+ st.selectbox('Timezone', options=tZoneList, key='tzone')
+
+
+ #with st.expander('Instrument settings'):
+ st.text_input("Network", placeholder='AM', key='network')
+ st.text_input("Station", placeholder='RAC84', key='station')
+ st.text_input("Location", placeholder='00', key='loc')
+ st.text_input("Channels", placeholder='EHZ, EHE, EHN', key='channels')
+
+ #with st.expander('Location settings'):
+ st.text_input('X Coordinate', help='i.e., Longitude or Easting', key='xcoord')
+ st.text_input('Y Coordinate', help='i.e., Latitude or Northing', key='ycoord')
+ st.text_input('Z Coordinate', help='i.e., Elevation', key='elevation')
+ st.session_state.elev_unit = st.selectbox('Z Unit', options=['m', 'ft'], help='i.e., Elevation unit')
+ st.number_input('Depth', help='i.e., Depth of measurement below ground surface (not currently used)', key='depth')
+
+ st.text_input('CRS of Input Coordinates', help='Can be EPSG code or anything accepted by pyproj.CRS.from_user_input()', key='input_crs')
+ st.text_input('CRS for Export', help='Can be EPSG code or anything accepted by pyproj.CRS.from_user_input()', key='output_crs')
+ if verbose:
+ print_param(param2print)
+
+ #@st.experimental_dialog("Update Parameters to Fetch Data", width='large')
+ #def open_fd_dialog():
+ with fdSetTab:
+ if verbose:
+ print('Setting up fd tab, session state length: ', len(st.session_state.keys()))
+ #source: str = 'file',
+ st.selectbox('Source', options=['File', 'Raw', 'Directory', "Batch"], index=0, key='source')
+ st.text_input('Trim Directory', help='Directory for saving trimmed data', key='trim_dir')
+ st.selectbox('Data format', options=OBSPYFORMATS, index=11, key='data_export_format')
+ st.selectbox('Detrend horizontal_method', options=['None', 'Simple', 'Linear', 'Constant/Demean', 'Polynomial', 'Spline'], index=5, help='Detrend horizontal_method use by `type` parameter of obspy.trace.Trace.detrend()', key='detrend')
+ st.text_input('Detrend options', value='detrend_options=2', help="Comma separated values with equal sign between key/value of arguments to pass to the **options argument of obspy.trace.Trace.detrend()", key='detrend_options')
+ if verbose:
+ print_param(param2print)
+
+
+ #@st.experimental_dialog("Update Parameters to Generate PPSDs", width='large')
+ #def open_ppsd_dialog():
+ with gpSetTab:
+ if verbose:
+ print('Setting up ppsd tab, session state length: ', len(st.session_state.keys()))
+ st.toggle('Skip on gaps', help='Determines whether time segments with gaps should be skipped entirely. Select skip_on_gaps=True for not filling gaps with zeros which might result in some data segments shorter than ppsd_length not used in the PPSD.',
+ key='skip_on_gaps')
+ st.number_input("Minimum Decibel Value", value=-200, step=1, key='min_deb')
+ st.number_input("Maximum Decibel Value", value=-50, step=1, key='max_deb')
+ st.number_input("Decibel bin size", value=1.0, step=0.1, key='deb_step')
+ st.session_state.db_bins = (st.session_state.min_deb, st.session_state.max_deb, st.session_state.deb_step)
+
+ st.number_input('PPSD Length (seconds)', step=1, key='ppsd_length')
+ st.number_input('PPSD Window overlap (%, 0-1)', step=0.01, min_value=0.0, max_value=1.0, key='overlap')
+ st.number_input('Period Smoothing Width (octaves)', step=0.1, key='period_smoothing_width_octaves')
+ st.number_input('Period Step (octaves)', step=0.005, format="%.5f", key='period_step_octaves')
+ periodVals=[round(1/x,3) for x in bandVals]
+ periodVals.sort()
+
+ st.select_slider('Period Limits (s)', options=periodVals, value=st.session_state.period_limits, key='period_limits')
+ st.selectbox("Special Handling", options=['None', 'Ringlaser', 'Hydrophone'], key='special_handling')
+ if verbose:
+ print_param(param2print)
+
+ #@st.experimental_dialog("Update Parameters to Remove Noise and Outlier Curves", width='large')
+ #def open_outliernoise_dialog():
+ with rmnocSetTab:
+ if verbose:
+ print('Setting up noise tab, session state length: ', len(st.session_state.keys()))
+ st.number_input("Outlier Threshold", value=98, key='rmse_thresh')
+ st.radio('Threshold type', options=['Percentile', 'Value'], key='threshRadio')
+ st.session_state.use_percentile = st.session_state.threshRadio=='Percentile'
+ st.radio('Threshold curve', options=['HV Curve', 'Component Curves'], key='curveRadio')
+ st.session_state.use_hv_curve = (st.session_state.curveRadio=='HV Curve')
+
+ st.multiselect("Noise Removal Method",
+ options=['None','Auto', 'Manual', 'Stalta', 'Saturation Threshold', 'Noise Threshold', 'Warmup', 'Cooldown', 'Buffer'], key='remove_method')
+ st.number_input('Saturation Percent', min_value=0.0, max_value=1.0, step=0.01, format="%.3f", key='sat_percent')
+ st.number_input('Noise Percent', min_value=0.0, max_value=1.0, step=0.1, format="%.2f", key='noise_percent')
+ st.number_input('Short Term Average (STA)', step=1.0, format="%.1f", key='sta')
+ st.number_input('Long Term Average (LTA)', step=1.0, format="%.1f", key='lta')
+ staltaVals = np.arange(0, 51).tolist()
+ st.select_slider('STA/LTA Thresholds', value=st.session_state.stalta_thresh, options=staltaVals, key='stalta_thresh')
+ st.number_input('Warmup Time (seconds)', step=1, key='warmup')
+ st.number_input('Cooldown Time (seconds)', step=1, key='cooldown')
+ st.number_input('Minimum Window Size (samples)', step=1, key='min_win_size')
+ st.toggle("Remove Raw Noise", help='Whether to use the raw input data to remove noise.', key='remove_raw_noise')
+ if verbose:
+ print_param(param2print)
+
+ #@st.experimental_dialog("Update Parameters to Process HVSR", width='large')
+ #def open_processHVSR_dialog():
+ with phvsrSetTab:
+ if verbose:
+ print('Setting up hvsr tab, session state length: ', len(st.session_state.keys()))
+ st.selectbox('Peak Selection Method', options=['Max', 'Scored'], key='peak_selection')
+ st.selectbox("Method to combine hoizontal components",
+ options=['Diffuse Field Assumption', 'Arithmetic Mean', 'Geometric Mean', 'Vector Summation', 'Quadratic Mean', 'Maximum Horizontal Value', 'Azimuth'],
+ index=2, key='horizontal_method')
+ rList = np.arange(1001).tolist()
+ rList[0] = False
+ st.selectbox("Curve Smoothing", options=['None', 'Savgoy Filter', 'Konno Ohmachi', "Proportional", "Constant"], index=2, key='freq_smooth')
+ st.select_slider("Curve Smoothing Parameter", options=np.arange(1000).tolist(), value=40, key='f_smooth_width')
+ st.select_slider("Resample", options=rList, value=1000, key='resample')
+ st.select_slider('Outlier Curve Removal', options=rList[:100], key='outlier_curve_rmse_percentile')
+ if verbose:
+ print_param(param2print)
+
+ def update_plot_string():
+ plotStringDict={'Peak Frequency':' p', 'Peak Amplitude':' pa', 'Annotation':' ann',
+ 'Time windows':' t', "Peaks of Time Windows": ' tp',
+ 'Test 1: Peak > 2x trough below':'1',
+ "Test 2: Peak > 2x trough above":'2',
+ "Test 3: Peak > 2":'3',
+ "Test 4":'4', "Test 5":'5', "Test 6":'6',
+ }
+
+ plotString = ''
+ for plot in st.session_state.plotPlotStr:
+ if plot=='HVSR':
+ plotString=plotString+'HVSR'
+ for pc in st.session_state.hvsrPlotStr:
+ if 'test' in pc.lower():
+ if 'test' not in plotString.lower():
+ plotString = plotString + ' Test'
+ test_end_index = plotString.rfind("Test") + len("Test")
+ nextSpaceIndex = plotString[test_end_index:].rfind(" ")
+ if nextSpaceIndex == -1:
+ nextSpaceIndex=len(plotString)
+ noString = plotString[test_end_index:nextSpaceIndex]
+ noString = noString + plotStringDict[pc]
+
+ # Order test numbers correctly
+ testNos = ''.join(sorted(noString))
+ plotString = plotString[:test_end_index] + testNos
+
+ else:
+ plotString = plotString + plotStringDict[pc]
+ if plot=='Components':
+ plotString=plotString+' C+'
+ for pc in st.session_state.compPlotStr:
+ plotString = plotString + plotStringDict[pc]
+ if plot=='Spectrogram':
+ plotString=plotString+' SPEC'
+ for pc in st.session_state.specPlotStr:
+ plotString = plotString + plotStringDict[pc]
+ if plot=='Azimuth':
+ plotString=plotString+' AZ'
+ st.session_state.plot_type = plotString
+
+
+ #@st.experimental_dialog("Update Plot Settings", width='large')
+ #def plot_settings_dialog():
+ with plotSetTab:
+ if verbose:
+ print('Setting up plot tab, session state length: ', len(st.session_state.keys()))
+
+ st.selectbox("Plot Engine (currently only plotly supported)", options=['Matplotlib', "Plotly"], key='plot_engine', disabled=True)
+ st.text_input("Plot type (plot string)", value='HVSR p ann C+ p ann Spec p', key='plot_type')
+ st.multiselect("Charts to show", options=['HVSR', "Components", 'Spectrogram', 'Azimuth'], default=['HVSR', 'Components', "Spectrogram"],
+ on_change=update_plot_string, key='plotPlotStr')
+
+ st.header("HVSR Chart", divider='rainbow')
+ st.multiselect('Items to plot', options=['Peak Frequency', 'Peak Amplitude', 'Annotation', 'Time windows', "Peaks of Time Windows",
+ 'Test 1: Peak > 2x trough below' , "Test 2: Peak > 2x trough above", "Test 3: Peak > 2", "Test 4", "Test 5", "Test 6"],
+ on_change=update_plot_string,
+ default=["Peak Frequency", "Annotation"], key='hvsrPlotStr')
+
+ st.header("Component Chart", divider='rainbow')
+ st.multiselect('Items to plot', options=['Peak Frequency', 'Annotation', 'Time windows'], on_change=update_plot_string,
+ default=["Peak Frequency", "Annotation"], key='compPlotStr')
+
+ st.header('Spectrogram Chart', divider='rainbow')
+ st.multiselect('Items to plot', options=['Peak Frequency', 'Annotation'], key='specPlotStr', on_change=update_plot_string)
+ if verbose:
+ print_param(param2print)
+
+ if verbose:
+ print('Done setting up sidebar, session state length: ', len(st.session_state.keys()))
+ print('Done setting up everything (end of main), session state length: ', len(st.session_state.keys()))
+ print_param(param2print)
+ #if __name__ == "__main__":
+ # main()
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/docs/_build/html/_modules/sprit/sprit_tkinter_ui.html b/docs/_build/html/_modules/sprit/sprit_tkinter_ui.html
index a120b9d..986b712 100644
--- a/docs/_build/html/_modules/sprit/sprit_tkinter_ui.html
+++ b/docs/_build/html/_modules/sprit/sprit_tkinter_ui.html
@@ -3,7 +3,7 @@
- sprit.sprit_tkinter_ui — sprit 2.0 documentation
+ sprit.sprit_tkinter_ui — sprit 2.1-dev documentation
@@ -12,7 +12,7 @@
-
+
diff --git a/docs/_build/html/_modules/sprit/sprit_utils.html b/docs/_build/html/_modules/sprit/sprit_utils.html
index f4b91c5..547842d 100644
--- a/docs/_build/html/_modules/sprit/sprit_utils.html
+++ b/docs/_build/html/_modules/sprit/sprit_utils.html
@@ -3,7 +3,7 @@
- sprit.sprit_utils — sprit 2.0 documentation
+ sprit.sprit_utils — sprit 2.1-dev documentation
@@ -12,7 +12,7 @@
-
+
@@ -436,7 +436,7 @@ Source code for sprit.sprit_utils
# Get fuller traceback information on errors
-def _get_error_from_exception(exception=None):
+def _get_error_from_exception(exception=None, print_error_message=True, return_error_message=False):
if exception is not None:
traceback.print_exception(sys.exc_info()[1])
exc_type, exc_obj, tb = sys.exc_info()
@@ -446,8 +446,13 @@ Source code for sprit.sprit_utils
errLineNo = str(traceback.extract_tb(sys.exc_info()[2])[-1].lineno)
error_category = type(exception).__name__.title().replace('error', 'Error')
error_message = f"{exception} ({errLineNo})"
- print(f"{error_category} ({errLineNo}): {error_message}")
- print(lineno, filename, f)
+
+ if print_error_message:
+ print(f"{error_category} ({errLineNo}): {error_message}")
+ print(lineno, filename, f)
+
+ if return_error_message:
+ return f"{error_category} ({errLineNo}): {error_message}\n\n{lineno} {filename} {f}"
#Check that input strema has Z, E, N channels
diff --git a/docs/_build/html/_sources/sprit.rst.txt b/docs/_build/html/_sources/sprit.rst.txt
index 5a45a00..1f8ef33 100644
--- a/docs/_build/html/_sources/sprit.rst.txt
+++ b/docs/_build/html/_sources/sprit.rst.txt
@@ -12,6 +12,7 @@ Submodules
.. toctree::
:maxdepth: 4
+ sprit.sprit_calibration
sprit.sprit_cli
sprit.sprit_hvsr
sprit.sprit_jupyter_UI
diff --git a/docs/_build/html/_sources/sprit.sprit_calibration.rst.txt b/docs/_build/html/_sources/sprit.sprit_calibration.rst.txt
new file mode 100644
index 0000000..1ff86db
--- /dev/null
+++ b/docs/_build/html/_sources/sprit.sprit_calibration.rst.txt
@@ -0,0 +1,7 @@
+sprit.sprit\_calibration module
+===============================
+
+.. automodule:: sprit.sprit_calibration
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js
index bca7572..32144d7 100644
--- a/docs/_build/html/_static/documentation_options.js
+++ b/docs/_build/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
const DOCUMENTATION_OPTIONS = {
- VERSION: '2.0',
+ VERSION: '2.1-dev',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
index db749d1..4c0d6d5 100644
--- a/docs/_build/html/genindex.html
+++ b/docs/_build/html/genindex.html
@@ -3,7 +3,7 @@
- Index — sprit 2.0 documentation
+ Index — sprit 2.1-dev documentation
@@ -12,7 +12,7 @@
-
+
@@ -90,6 +90,8 @@ Index
| R
| S
| T
+ | U
+ | W
| X
@@ -132,6 +134,18 @@ C
+
+