diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 23e4849a..095b1134 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -22,14 +22,14 @@ repos: - id: check-ast - id: check-case-conflict - id: trailing-whitespace - exclude: ".*(.fits|.fts|.fit|.txt|.pro)$" + exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.json)$" - id: check-yaml - id: debug-statements - id: check-added-large-files - id: end-of-file-fixer - exclude: ".*(.fits|.fts|.fit|.txt|.pro|.bib|tca.*)$" + exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.json|.bib|tca.*)$" - id: mixed-line-ending - exclude: ".*(.fits|.fts|.fit|.txt|.bib|tca.*)$" + exclude: ".*(.fits|.fts|.fit|.txt|.bib|.pro|.asdf|.json|tca.*)$" - repo: https://github.com/codespell-project/codespell rev: v2.2.6 diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 00000000..3a650494 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,2 @@ +prune fiasco/test/idl/data +prune fiasco/test/idl/ssw_gen_functions diff --git a/fiasco/conftest.py b/fiasco/conftest.py index 5843f5ab..aa78284c 100644 --- a/fiasco/conftest.py +++ b/fiasco/conftest.py @@ -1,6 +1,9 @@ +import numpy as np import pathlib import pytest +from packaging.version import Version + from fiasco.util import check_database, read_chianti_version # Force MPL to use non-gui backends for testing. @@ -15,82 +18,250 @@ # Minimal set of CHIANTI files needed to run the tests # NOTE: need some way for this to be flexible depending on the supplied database version TEST_FILES = { - 'sun_coronal_1992_feldman_ext.abund': '8b18d62e03528e3b3800806a1fc9391e', - 'sun_coronal_1992_feldman.abund': '75fde4f73bae8fdce136f65b736bc0c8', - 'chianti.ip': 'a5a5071535f14590210957f8783f2843', - 'chianti.ioneq': '81d8d24bb09cb2da63befd30e6c8767c', - 'gffgu.dat': '5895e1f211e7baa8293478df014b9ff1', - 'gffint.dat': '96381825257793805ca42eba03ae83e2', - 'klgfb.dat': '5496daa096dd4f7b935ec0d0e6417084', - 'itoh.dat': 'e40aacc9d06889f9c4ba63a92673a398', - 'hseq_2photon.dat': '48656984fbcbe38f883ff9a4460c790a', - 'heseq_2photon.dat': '9e42ac8c37d67ba3109aaa56aab9e736', - 'verner_short.txt': 'f05296ffc9c5306846ac9caf136fad26', - 'flare.dem': '1eb949e8c7fd2cb3e9e6903e85d86217', - 'h_1.elvlc': 'd31620aaf26a14486e635d14bcf7a6c1', - 'h_1.wgfa': 'ed2a561ecdba5ee4b05ea56c297724ba', - 'h_1.scups': 'de180c9e1b4f50a503efad8c83e714ab', - 'h_1.diparams': 'f9be79794cc092c75733ece7aba9f29f', - 'h_1.fblvl': 'af45fd1ee7af4b4e71aba288d0b16bc8', - 'h_2.rrparams': '05eb5044dc1ad070338d1ba3745dc4de', - 'he_1.elvlc': '577245da46cfc4d27a05f40147f17610', - 'he_2.elvlc': '58eee740f6842850f1f35a4f95b3e12c', - 'he_3.rrparams': '67e2e7a5e86c8eaa5db4e95ac3d35989', - 'c_1.diparams': '18e24ef4119abccd7226871045ebf769', - 'c_2.diparams': '499271a2634a66e6d0717f97cf1f6e7a', - 'c_2.drparams': 'b9adf6474864b7d480c2132a95099358', - 'c_2.rrparams': '04c6cab3710f847f40e751e23fe29a54', - 'c_3.diparams': 'e573d3ad1b34f86ef2896813a8452d4e', - 'c_3.drparams': '3d1d3b00866e77d51afd1206a6c63989', - 'c_3.easplups': '8281d99bfd4d9165302ca9b27c219d41', - 'c_3.rrparams': '8122c689559acd7715bd12a86672fb8f', - 'c_4.diparams': 'a6f236513ffd130bfbab9a222c52e451', - 'c_4.drparams': 'd2435409c5a86c4ff4e9687255d2d9f4', - 'c_4.easplups': 'e9574be2d6434adcebbead5efdd6b638', - 'c_4.rrparams': '1bcd165f366b6e48c550ff4b841eb4d7', - 'c_5.diparams': '8087926a840a5da8c20a9eb36645316a', - 'c_5.drparams': 'ff50ded77ec19c7a22f057663fff5c22', - 'c_5.rrparams': 'e35b12f4fedc6326c91f31a22e037e88', - 'c_6.diparams': '6bdf83507b516f50f9561cc253d735d4', - 'c_6.drparams': '56503cbd1ed960101eefeaff77b41392', - 'c_6.rrparams': '811014c5b1ee782e12bab6ea53f52f04', - 'c_6.elvlc': 'f64c0559e1e61fb44a521b75cf22d144', - 'c_6.wgfa': 'dac0a16a54664b454974ef6d67ba8fed', - 'c_6.scups': '55672bf604baf5fe46f537b44f019eaf', - 'c_6.psplups': '50232c7869cc71904ebc87aa62d4bc4a', - 'c_7.rrparams': '686156392d4cfabb3f0ff0280970f562', - 'ca_4.rrparams': '35f3713b90e6be7de6ca36c558546578', - 'ca_4.drparams': '7cbb34c0041aba833c389256863b66cc', - 'li_1.diparams': '2a4b60bc799a1ea3ee3e911b5968733e', - 'ca_2.elvlc': 'c8a9dbdc622d0a15eea6cf0eb1631d3b', - 'fe_2.elvlc': '9306d594a66b4649363a778a650853f9', - 'fe_5.elvlc': 'f7dd75c6bcea77584c5e00ddf2684d9c', - 'fe_5.fblvl': 'e13a9becff489ea044fbd3cb1e02af13', - 'fe_5.drparams': '0f47e2fbf4be9eb5564a8adc19531999', - 'fe_5.easplups': 'ec5443d429722ccdd9903743ca4718ab', - 'fe_5.scups': '0a863212d59c5eda5936e0664b513fb9', - 'fe_5.wgfa': '6f8e4d41760d5a0540008e15aca1038c', - 'fe_6.elvlc': '081519f986b8a8ed99a34ecf813f1358', - 'fe_6.fblvl': '9478aeab2479e9eefebfd1e552e27ddf', - 'fe_7.fblvl': 'ad0264f06018b0b9cca1eba502809708', - 'fe_9.elvlc': 'b7d04f65a87a8de1c2bfc77331e438f3', - 'fe_12.elvlc': 'ee9beb8b2ff03ba8fc046bd722992b21', - 'fe_15.elvlc': 'cb8e6291bac17325130ea8564e118d48', - 'fe_16.diparams': '8c7733d443eceab3e2fd4073bacfa9a5', - 'fe_16.drparams': '5067a1e2ed714c673681ac8e6d8325f7', - 'fe_16.easplups': '9de5fcdb0814dbb8e51a4aad18273229', - 'fe_16.rrparams': 'f5adaae054fd083a3a41d6bdddb06fa8', - 'fe_18.elvlc': 'e5384e1f58d689bd29f83eede58bc290', - 'fe_18.scups': 'ec57a94f781a3b6b553de90679e0a07c', - 'fe_18.wgfa': 'f58accd58b7de6342ee174bb844642b8', - 'fe_27.rrparams': '75383b0f1b167f862cfd26bbadd2a029', - 'fe_10.psplups': 'dd34363f6daa81dbf106fbeb211b457d', - 'fe_10.elvlc': 'f221d4c7167336556d57378ac368afc1', - 'fe_20.elvlc': 'bbddcf958dd41311ea24bf177c2b62de', - 'fe_20.wgfa': 'c991c30b98b03c9152ba5a2c71877149', - 'fe_20.scups': 'f0e375cad2ec8296efb2abcb8f02705e', - 'fe_20.cilvl': 'b71833c51a03c7073f1657ce60afcdbb', - 'fe_20.reclvl': 'cf28869709acef521fb6a1c9a2b59530', + 'sun_coronal_1992_feldman_ext.abund', + 'sun_coronal_1992_feldman.abund', + 'chianti.ip', + 'chianti.ioneq', + 'gffgu.dat', + 'gffint.dat', + 'klgfb.dat', + 'itoh.dat', + 'hseq_2photon.dat', + 'heseq_2photon.dat', + 'verner_short.txt', + 'flare.dem', + 'h_1.elvlc', + 'h_1.wgfa', + 'h_1.scups', + 'h_1.diparams', + 'h_2.rrparams', + 'he_1.elvlc', + 'he_2.elvlc', + 'he_3.rrparams', + 'c_1.diparams', + 'c_2.diparams', + 'c_2.drparams', + 'c_2.rrparams', + 'c_3.diparams', + 'c_3.drparams', + 'c_3.easplups', + 'c_3.rrparams', + 'c_4.diparams', + 'c_4.drparams', + 'c_4.easplups', + 'c_4.rrparams', + 'c_5.diparams', + 'c_5.drparams', + 'c_5.rrparams', + 'c_6.diparams', + 'c_6.drparams', + 'c_6.rrparams', + 'c_6.elvlc', + 'c_6.wgfa', + 'c_6.scups', + 'c_6.psplups', + 'c_7.rrparams', + 'ca_4.rrparams', + 'ca_4.drparams', + 'ca_15.elvlc', + 'ca_15.wgfa', + 'ca_15.psplups', + 'ca_15.scups', + 'li_1.diparams', + 'ca_2.elvlc', + 'fe_2.elvlc', + 'fe_5.elvlc', + 'fe_5.drparams', + 'fe_5.easplups', + 'fe_5.scups', + 'fe_5.wgfa', + 'fe_6.elvlc', + 'fe_9.scups', + 'fe_9.wgfa', + 'fe_9.elvlc', + 'fe_9.fblvl', + 'fe_11.elvlc', + 'fe_11.wgfa', + 'fe_11.scups', + 'fe_11.psplups', + 'fe_12.elvlc', + 'fe_14.elvlc', + 'fe_14.wgfa', + 'fe_14.scups', + 'fe_14.psplups', + 'fe_15.elvlc', + 'fe_16.diparams', + 'fe_16.drparams', + 'fe_16.easplups', + 'fe_16.elvlc', + 'fe_16.scups', + 'fe_16.wgfa', + 'fe_16.rrparams', + 'fe_18.elvlc', + 'fe_18.scups', + 'fe_18.wgfa', + 'fe_27.rrparams', + 'fe_10.psplups', + 'fe_10.elvlc', + 'fe_20.elvlc', + 'fe_20.wgfa', + 'fe_20.scups', + 'fe_20.cilvl', + 'fe_20.reclvl', + 'he_2.fblvl', + 'he_1.fblvl', + 'ni_28.fblvl', + 'ni_17.fblvl', + 'ni_21.fblvl', + 'ni_19.fblvl', + 'ni_26.fblvl', + 'ni_18.fblvl', + 'ni_27.fblvl', + 'ni_20.fblvl', + 'ni_16.fblvl', + 'ni_11.fblvl', + 'ni_13.fblvl', + 'ni_25.fblvl', + 'ni_22.fblvl', + 'ni_23.fblvl', + 'ni_24.fblvl', + 'ni_12.fblvl', + 'ni_15.fblvl', + 'al_13.fblvl', + 'al_12.fblvl', + 'al_9.fblvl', + 'al_7.fblvl', + 'al_1.fblvl', + 'al_6.fblvl', + 'al_8.fblvl', + 'al_10.fblvl', + 'al_11.fblvl', + 'al_3.fblvl', + 'al_4.fblvl', + 'al_5.fblvl', + 'mg_7.fblvl', + 'mg_9.fblvl', + 'mg_8.fblvl', + 'mg_1.fblvl', + 'mg_6.fblvl', + 'mg_10.fblvl', + 'mg_11.fblvl', + 'mg_3.fblvl', + 'mg_4.fblvl', + 'mg_5.fblvl', + 'mg_2.fblvl', + 'mg_12.fblvl', + 'ca_17.fblvl', + 'ca_10.fblvl', + 'ca_19.fblvl', + 'ca_20.fblvl', + 'ca_18.fblvl', + 'ca_11.fblvl', + 'ca_16.fblvl', + 'ca_13.fblvl', + 'ca_14.fblvl', + 'ca_15.fblvl', + 'ca_12.fblvl', + 'ca_9.fblvl', + 'fe_10.fblvl', + 'fe_17.fblvl', + 'fe_21.fblvl', + 'fe_26.fblvl', + 'fe_19.fblvl', + 'fe_18.fblvl', + 'fe_20.fblvl', + 'fe_16.fblvl', + 'fe_11.fblvl', + 'fe_5.fblvl', + 'fe_4.fblvl', + 'fe_14.fblvl', + 'fe_13.fblvl', + 'fe_25.fblvl', + 'fe_22.fblvl', + 'fe_23.fblvl', + 'fe_24.fblvl', + 'fe_12.fblvl', + 'fe_15.fblvl', + 'fe_8.fblvl', + 'fe_6.fblvl', + 'fe_7.fblvl', + 'fe_9.fblvl', + 'n_3.fblvl', + 'n_4.fblvl', + 'n_5.fblvl', + 'n_2.fblvl', + 'n_7.fblvl', + 'n_1.fblvl', + 'n_6.fblvl', + 's_6.fblvl', + 's_1.fblvl', + 's_8.fblvl', + 's_9.fblvl', + 's_7.fblvl', + 's_12.fblvl', + 's_15.fblvl', + 's_14.fblvl', + 's_13.fblvl', + 's_2.fblvl', + 's_5.fblvl', + 's_4.fblvl', + 's_3.fblvl', + 's_16.fblvl', + 's_11.fblvl', + 's_10.fblvl', + 'o_7.fblvl', + 'o_6.fblvl', + 'o_1.fblvl', + 'o_8.fblvl', + 'o_4.fblvl', + 'o_3.fblvl', + 'o_2.fblvl', + 'o_5.fblvl', + 'h_1.fblvl', + 'si_12.fblvl', + 'si_14.fblvl', + 'si_13.fblvl', + 'si_2.fblvl', + 'si_5.fblvl', + 'si_4.fblvl', + 'si_3.fblvl', + 'si_11.fblvl', + 'si_10.fblvl', + 'si_6.fblvl', + 'si_1.fblvl', + 'si_8.fblvl', + 'si_9.fblvl', + 'si_7.fblvl', + 'ar_10.fblvl', + 'ar_17.fblvl', + 'ar_16.fblvl', + 'ar_11.fblvl', + 'ar_18.fblvl', + 'ar_4.fblvl', + 'ar_8.fblvl', + 'ar_1.fblvl', + 'ar_14.fblvl', + 'ar_13.fblvl', + 'ar_7.fblvl', + 'ar_9.fblvl', + 'ar_12.fblvl', + 'ar_15.fblvl', + 'ne_9.fblvl', + 'ne_7.fblvl', + 'ne_6.fblvl', + 'ne_1.fblvl', + 'ne_8.fblvl', + 'ne_4.fblvl', + 'ne_10.fblvl', + 'ne_3.fblvl', + 'ne_2.fblvl', + 'ne_5.fblvl', + 'c_5.fblvl', + 'c_2.fblvl', + 'c_3.fblvl', + 'c_4.fblvl', + 'c_1.fblvl', + 'c_6.fblvl', } @@ -121,10 +292,8 @@ def hdf5_dbase_root(ascii_dbase_tree, tmpdir_factory, request): if request.config.getoption('--include-all-files'): test_files = None else: - if request.config.getoption('--disable-file-hash'): - test_files = [k for k in TEST_FILES] - else: - test_files = TEST_FILES + test_files = TEST_FILES + check_hash = not request.config.getoption('--disable-file-hash') # Optionally use a different URL for the database (e.g. for testing different versions) ascii_dbase_url = request.config.getoption('--ascii-dbase-url') # Optionally disable version checking. This is useful when testing newer/older versions @@ -136,7 +305,8 @@ def hdf5_dbase_root(ascii_dbase_tree, tmpdir_factory, request): ask_before=False, ascii_dbase_url=ascii_dbase_url, check_chianti_version=check_chianti_version, - files=test_files) + files=test_files, + check_hash=check_hash) return path @@ -160,14 +330,24 @@ def requires_dbase_version(request, dbase_version): # NOTE: Fixtures that depend on other fixtures are awkward to implement. # See this SO answer: https://stackoverflow.com/a/28198398 if marker := request.node.get_closest_marker('requires_dbase_version'): - version_condition = marker.args[0] - # NOTE: This currently only works for major versions. If we - # need tests that discriminate between minor versions or patches, - # this logic will need to be added. - conditional = f'{dbase_version["major"]}{version_condition}' - allowed_dbase_version = eval(conditional) + # NOTE: This has to have a space between the operator and the target + if len(marker.args) != 2: + raise ValueError("Arguments must contain a condition and a version number, e.g. '<', '8.0.7'") + operator, target_version = marker.args + op_dict = {'<': np.less, + '<=': np.less_equal, + '>': np.greater, + '>=': np.greater_equal, + '=': np.equal, + '==': np.equal, + '!=': np.not_equal} + if operator not in op_dict: + raise ValueError(f'''{operator} is not a supported comparison operation. + Must be one of {list(op_dict.keys())}.''') + target_version = Version(target_version) + allowed_dbase_version = op_dict[operator](dbase_version, target_version) if not allowed_dbase_version: - pytest.skip(f'Test skipped because current dbase version {conditional}.') + pytest.skip(f'Skip because database version {dbase_version} is not {operator} {target_version}.') def pytest_configure(config): diff --git a/fiasco/io/generic.py b/fiasco/io/generic.py index c74e9faa..e271eed8 100644 --- a/fiasco/io/generic.py +++ b/fiasco/io/generic.py @@ -34,7 +34,7 @@ def __init__(self, filename, **kwargs): self.chianti_version = '' else: version = read_chianti_version(self.ascii_dbase_root) - self.chianti_version = f"{version['major']}.{version['minor']}.{version['patch']}" + self.chianti_version = f"{version}" self.full_path = pathlib.Path(filename) if standalone else self.ascii_dbase_root / self.filename def parse(self): diff --git a/fiasco/io/sources/tests/test_sources.py b/fiasco/io/sources/tests/test_sources.py index 02d039b2..bd1d291d 100644 --- a/fiasco/io/sources/tests/test_sources.py +++ b/fiasco/io/sources/tests/test_sources.py @@ -22,8 +22,8 @@ 'fe_2.trparams', 'fe_12.drparams', 'al_3.diparams', - pytest.param('fe_23.auto', marks=pytest.mark.requires_dbase_version('>=9')), - pytest.param('fe_23.rrlvl', marks=pytest.mark.requires_dbase_version('>=9')), + pytest.param('fe_23.auto', marks=pytest.mark.requires_dbase_version('>=', '9')), + pytest.param('fe_23.rrlvl', marks=pytest.mark.requires_dbase_version('>=', '9')), ]) def test_ion_sources(ascii_dbase_root, filename,): parser = fiasco.io.Parser(filename, ascii_dbase_root=ascii_dbase_root) diff --git a/fiasco/tests/coveragerc b/fiasco/tests/coveragerc deleted file mode 100644 index 3768a824..00000000 --- a/fiasco/tests/coveragerc +++ /dev/null @@ -1,30 +0,0 @@ -[run] -source = fiasco -omit = - fiasco/conftest* - fiasco/cython_version* - fiasco/setup_package* - fiasco/*/setup_package* - fiasco/*/*/setup_package* - fiasco/tests/* - fiasco/*/tests/* - fiasco/*/*/tests/* - fiasco/version* - -[report] -exclude_lines = - # Have to re-enable the standard pragma - pragma: no cover - - # Don't complain about packages we have installed - except ImportError - - # Don't complain if tests don't hit assertions - raise AssertionError - raise NotImplementedError - - # Don't complain about script hooks - def main\(.*\): - - # Ignore branches that don't pertain to this version of Python - pragma: py{ignore_python_version} diff --git a/fiasco/tests/idl/conftest.py b/fiasco/tests/idl/conftest.py index 3c348b9d..6198a248 100644 --- a/fiasco/tests/idl/conftest.py +++ b/fiasco/tests/idl/conftest.py @@ -6,16 +6,18 @@ @pytest.fixture(scope="session") def idl_env(ascii_dbase_root, request): + # NOTE: The reason that we return None here rather than calling pytest.skip + # is that the IDL tests can still be run if there is a file containing the IDL + # results available. Thus, we have to wait until later to decide if we want to + # skip the test. idl_executable = request.config.getoption('--idl-executable') idl_codebase_root = request.config.getoption('--idl-codebase-root') - if idl_codebase_root is None or idl_codebase_root is None: - pytest.skip('''Must specify path to IDL executable and CHIANTI IDL code in order to - run the IDL comparison tests.''') + if idl_executable is None or idl_codebase_root is None: + return None try: import hissw except ImportError: - pytest.skip('''The hissw package is required to install the IDL comparison tests. - See https://github.com/wtbarnes/hissw for installation information.''') + return None extra_paths = [d for d, _, _ in os.walk(idl_codebase_root)] header = f''' defsysv,'!xuvtop','{ascii_dbase_root}' @@ -32,7 +34,6 @@ def idl_env(ascii_dbase_root, request): try: _ = env.run('print,!xuvtop') except (hissw.util.SSWIDLError, hissw.util.IDLLicenseError): - pytest.skip('''Could not configure CHIANTI IDL environment. - You will not be able to run portions of the test suite.''') + return None else: return env diff --git a/fiasco/tests/idl/data/freebound_all_ions_v8.0.7.asdf b/fiasco/tests/idl/data/freebound_all_ions_v8.0.7.asdf new file mode 100644 index 00000000..6b4d9d8a Binary files /dev/null and b/fiasco/tests/idl/data/freebound_all_ions_v8.0.7.asdf differ diff --git a/fiasco/tests/idl/data/freefree_all_ions_v8.0.7.asdf b/fiasco/tests/idl/data/freefree_all_ions_v8.0.7.asdf new file mode 100644 index 00000000..0d7b886c Binary files /dev/null and b/fiasco/tests/idl/data/freefree_all_ions_v8.0.7.asdf differ diff --git a/fiasco/tests/idl/data/goft_20_15_200.972_v8.0.7.asdf b/fiasco/tests/idl/data/goft_20_15_200.972_v8.0.7.asdf new file mode 100644 index 00000000..9160c28d Binary files /dev/null and b/fiasco/tests/idl/data/goft_20_15_200.972_v8.0.7.asdf differ diff --git a/fiasco/tests/idl/data/goft_26_11_188.497_v8.0.7.asdf b/fiasco/tests/idl/data/goft_26_11_188.497_v8.0.7.asdf new file mode 100644 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a/fiasco/tests/idl/data/ioneq_6_3_v8.0.7.asdf b/fiasco/tests/idl/data/ioneq_6_3_v8.0.7.asdf new file mode 100644 index 00000000..98332e98 Binary files /dev/null and b/fiasco/tests/idl/data/ioneq_6_3_v8.0.7.asdf differ diff --git a/fiasco/tests/idl/helpers.py b/fiasco/tests/idl/helpers.py new file mode 100644 index 00000000..021fc731 --- /dev/null +++ b/fiasco/tests/idl/helpers.py @@ -0,0 +1,80 @@ +""" +Helpers for tests related to comparing with IDL output +""" +import pathlib +import pytest + +from astropy.utils.data import get_pkg_data_path + +__all__ = ['get_idl_test_output_filepath', 'read_idl_test_output', 'run_idl_script'] + + +def get_idl_test_output_filepath(name, version): + data_dir = pathlib.Path(get_pkg_data_path('data', package='fiasco.tests.idl')) + return data_dir / f"{name}_v{version}.asdf" + + +def read_idl_test_output(name, version, keys=None): + # NOTE: Importing here to avoid it as a hard dependency for running tests + import asdf + file_path = get_idl_test_output_filepath(name, version) + with asdf.open(file_path, copy_arrays=True) as af: + if keys is None: + keys = af.tree.keys() + output = {k: af.tree[k] for k in keys} + return output + + +def run_idl_script(idl_env, script, input_args, save_vars, file_name, version, format_func=None, write_file=True): + """ + Helper function for running CHIANTI IDL via hissw in tests + + This function runs the IDL script with hissw and saves the output to an asdf file + such that tests can be run to compare against the IDL results without actually rerunning + the IDL code. If the output file already exists, then the results are read from that file. + + Parameters + ---------- + idl_env: `hissw.Environment` + IDL environment to use to run the test script + script: `str` + IDL script to run to generate test comparison data + input_args: `dict` + All inputs to the IDL script + save_vars: `list` + List of variables to return from the IDL calculation + file_name: `str` + Name of the IDL results file + version: `packaging.version.Version`, `str` + Version of IDL used to generate these test results + format_func: `dict`, optional + Functions to use to format output from the IDL function. + This is most useful for adding the necessary units to any of the outputs. + write_file: `bool`, optional + If True, writes the result to a file so that the test can be run later without + an IDL installation. If False, running this test will always require an IDL + installation. Setting this to False may be needed to reduce the amount of test + data. + """ + # NOTE: Importing here to avoid it as a hard dependency for running tests + import asdf + file_path = get_idl_test_output_filepath(file_name, version) + if not file_path.is_file(): + if idl_env is None: + pytest.skip("""To run the IDL comparison tests, you must: + 1. Specify a path to a working IDL executable, + 2. Specify a path to the CHIANTI IDL code, + 3. Install the hissw package (pip install hissw) + Without the following, you will not be able to generate new IDL comparison test results.""") + result = idl_env.run(script, args=input_args, save_vars=save_vars) + if format_func is not None: + for k in format_func: + result[k] = format_func[k](result[k]) + # Save the the contribution function to the data directory + variables = {**result, **input_args, 'idl_script': script} + if write_file: + with asdf.AsdfFile(variables) as af: + af.write_to(file_path) + else: + return variables + return read_idl_test_output(file_name, version) diff --git a/fiasco/tests/idl/ssw_gen_functions/datatype.pro b/fiasco/tests/idl/ssw_gen_functions/datatype.pro new file mode 100644 index 00000000..f2e7170b --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/datatype.pro @@ -0,0 +1,156 @@ +function datatype,var, flag0, descriptor=desc, help=hlp, Tname = tname + ;+ +; NAME: +; DATATYPE() +; +; PURPOSE: +; Returns the data type of a variable. +; +; EXPLANATION: +; This routine returns the data type of a variable in a format specified +; by the optional flag parameter. Can also be used to emulate, in +; earlier versions of IDL, the SIZE(/TNAME) option introduced in V5.1. +; +; This routine was originally derived from the JHUAPL library ***but has +; diverged from the JHUAPL library for the newer data types.*** For this +; reason DATATYPE is no longer used in any other procedure in the IDL +; Astronomy Library. +; CALLING SEQUENCE : +; Result = DATATYPE( VAR [, FLAG , /TNAME, /DESC ] ) +; +; INPUTS: +; VAR = Variable to examine, no restrictions +; +; OPTIONAL INPUT PARAMETERS: +; FLAG = Integer between 0 and 3 giving the output format flag as +; explained below. The default is 0. +; /DESC = If set, then return a descriptor for the given variable. If the +; variable is a scalar the value is returned as a string. If it is +; an array a description is returned just like the HELP command +; gives. Ex:' +; IDL> print, datatype(fltarr(2,3,5),/desc) gives the string +; 'FLTARR(2,3,5)' +; /TNAME - If set, then returns a identical result to the use of the /TNAME +; keyword to the SIZE() function in IDL V5.2 and later. +; Overrides the value of FLAG. +; /HELP = If set, then a short explanation is printed out. +; +; OUTPUT PARAMETERS: +; The result of the function is the either a string or integer giving the +; data type of VAR. Depending on the value of FLAG or /TNAME, the result +; will be one of the values from the following table: +; +; FLAG = 0 FLAG = 1 FLAG = 2 FLAG = 3 /TNAME +; +; UND Undefined 0 UND UNDEFINED +; BYT Byte 1 BYT BYTE +; INT Integer 2 INT INT +; LON Long 3 LON LONG +; FLO Float 4 FLT FLOAT +; DOU Double 5 DBL DOUBLE +; COM Complex 6 COMPLEX COMPLEX +; STR String 7 STR STRING +; STC Structure 8 STC STRUCT +; DCO DComplex 9 DCOMPLEX DCOMPLEX +; PTR Pointer 10 PTR POINTER +; OBJ Object 11 OBJ OBJREF +; UIN UInt 12 UINT UINT +; ULN ULong 13 ULON ULONG +; L64 Long64 14 LON64 LONG64 +; U64 ULong64 15 ULON64 ULONG64 +; +; +; REVISION HISTORY: +; Original Version: R. Sterner, JHU/APL, 24 October 1985. +; Major rewrite, add /TNAME keyword, unsigned and 64 bit datatypes +; W. Landsman August 1999 +; Zarro (SM&A/GSFC) - November 2001, replace error stops by continues +;- +;------------------------------------------------------------- + + + if (N_params() lt 1) or keyword_set(hlp) then begin + print,' Datatype of variable as a string (3 char or spelled out).' + print,' typ = datatype(var, [flag])' + print,' var = variable to examine. in' + print,' flag = output format flag (def=0). in' + print,' typ = datatype string or number. out' + print,' flag=0 flag=1 flag=2 flag=3 /TNAME' + print,' UND Undefined 0 UND UNDEFINE' + print,' BYT Byte 1 BYT BYTE' + print,' INT Integer 2 INT INT' + print,' LON Long 3 LON LONG' + print,' FLO Float 4 FLT FLOAT' + print,' DOU Double 5 DBL DOUBLE' + print,' COM Complex 6 COMPLEX COMPLEX' + print,' STR String 7 STR STRING' + print,' STC Structure 8 STC STRUCT' + print,' DCO DComplex 9 DCOMPLEX DCOMPLEX' + print,' PTR Pointer 10 PTR POINTER' + print,' OBJ Object 11 OBJ OBJREF' + print,' UIN UInt 12 UINT UINT' + print,' ULO ULong 13 ULON ULONG' + print,' L64 Long64 14 LON64 LONG64' + print,' U64 ULong64 15 ULON64 ULONG64' + print,' Keywords:' + print,' /TNAME - Identical output to SIZE(/TNAME) ' + print,' /DESCRIPTOR returns a descriptor for the given variable.' + print,' If the variable is a scalar the value is returned as' + print,' a string. If it is an array a description is return' + print,' just like the HELP command gives. Ex:' + print,' datatype(fltarr(2,3,5),/desc) gives' + print,' FLTARR(2,3,5) (flag always defaults to 3 for /DESC).' + return, -1 + endif + + s_tname = ['UNDEFINE', 'BYTE','INT','LONG','FLOAT','DOUBLE','COMPLEX',$ + 'STRING','STRUCT','DCOMPLEX','POINTER','OBJREF','UINT','ULONG', $ + 'LONG64','ULONG64'] + + s_flag0 = ['UND','BYT','INT','LON','FLO','DOU','COM','STR','STC','DCO','PTR',$ + 'OBJ','UIN','ULO','L64','U64'] + + s_flag1 = ['Undefined','Byte','Integer','Long','Float','Double','Complex', $ + 'String','Structure','DComplex','Pointer','Object','UInt','ULong',$ + 'Long64','ULong64'] + + s_flag3 = [ 'UND','BYT','INT','LON','FLT','DBL','COMPLEX','STR','STC', $ + 'DCOMPLEX','PTR','OBJ','UINT','ULON','LON64','ULON64'] + + s = size(var) + stype = s[s[0]+1] + if stype GT N_elements(s_tname) then begin + message,'ERROR - Unrecognized IDL datatype',/cont + stype=0 + endif + + if keyword_set(TNAME) then return, s_tname[stype] + + if N_params() lt 2 then flag0 = 0 ; Default flag. + if keyword_set(desc) then flag0 = 3 + + case flag0 of + + 0: return, s_flag0[stype] + 1: return, s_flag1[stype] + 2: return, stype + 3: typ = s_flag3[stype] + else: message,'ERROR - Flag parameter must be between 0 and 3' + endcase + + if keyword_set(desc) then begin + if stype EQ 0 then begin + message,'ERROR - Input variable is undefined',/cont + return,'Undefined' + endif + if s[0] eq 0 then return,strtrim(var,2) ; Return scalar desc. + aa = typ+'ARR(' + for i = 1, s[0] do begin + aa = aa + strtrim(s[i],2) + if i lt s[0] then aa = aa + ',' + endfor + aa = aa+')' + return, aa + endif else return,typ + + end diff --git a/fiasco/tests/idl/ssw_gen_functions/default.pro b/fiasco/tests/idl/ssw_gen_functions/default.pro new file mode 100755 index 00000000..8f397ad3 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/default.pro @@ -0,0 +1,50 @@ +;+ +; Project : SOHO - CDS +; +; Name : DEFAULT +; +; Purpose : Supply default values for variables +; +; Explanation : If the first parameter is not defined, it is +; set to the value of the second parameter. +; +; Use : DEFAULT,VARIABLE,DEFAULT_VALUE +; +; Inputs : VARIABLE : The variable that could take on the default value +; +; DEFAULT_VALUE : The default value. +; +; Opt. Inputs : None. +; +; Outputs : None. +; +; Opt. Outputs: None. +; +; Keywords : None. +; +; Calls : None. +; +; Common : None. +; +; Restrictions: None. +; +; Side effects: None. +; +; Category : Utility, Misc. +; +; Prev. Hist. : Taken from my private library. +; +; Written : Stein Vidar Hagfors Haugan +; +; Modified : Never +; +; Version : 1, 4-Sept-1995 +;- + +PRO DEFAULT,VAR,VAL + +If N_params() lt 2 then message,"Use: DEFAULT,VARIABLE,DEFAULT_VALUE" + +IF N_ELEMENTS(VAR) EQ 0 THEN VAR=VAL + +END diff --git a/fiasco/tests/idl/ssw_gen_functions/delvarx.pro b/fiasco/tests/idl/ssw_gen_functions/delvarx.pro new file mode 100644 index 00000000..64611b93 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/delvarx.pro @@ -0,0 +1,52 @@ +;+ +; NAME: +; DELVARX +; PURPOSE: +; Undefine up to 10 variables for memory management (can call from routines) +; EXPLANATION: +; Similar to the intrinsic DELVAR function, but can be used from any calling level. +; (DELVAR can only be used at the main level.) Note, however, that unlike DELVAR, +; DELVARX does not delete the variables (they will be listed as UNDEFINED when +; viewed with HELP), but only makes them undefined and frees their memory +; +; Also look at the similar Coyote routine UNDEFINE +; http://www.idlcoyote.com/programs/undefine.pro +; +; CALLING SEQUENCE: +; DELVARX, p0, [p1, p2......p9] +; +; INPUTS: +; p0, p1...p9 - variables to delete +; +; OBSOLETE KEYWORD: +; /FREE_MEM - free memory associated with pointers and objects. Since this is now the +; DELVARX default (since 2012) this keyword now does nothing. +; +; METHOD: +; Uses HEAP_FREE and PTR_NEW(/NO_COPY) to undefine variables and free memory +; +; REVISION HISTORY: +; Copied from the Solar library, written by slf, 25-Feb-1993 +; Added to Astronomy Library, September 1995 +; Modified, 26-Mar-2003, Zarro (EER/GSFC) 26-Mar-2003 +; - added FREE_MEM to free pointer/objects +; Modified, 28-Jan-2012, E. Rykoff (SLAC), W. Landsman - +; replace EXECUTE calls with SCOPE_VARFETCH. +; Clarified documentation W. Landsman Sep 2018 +;- + +PRO delvarx, p0,p1,p2,p3,p4,p5,p6,p7,p8,p9,free_mem = free_mem + + npar = N_params() ; Number of parameters + pp = 'p'+strtrim(indgen(npar),1) + + for i=0,npar-1 do begin + defined = N_elements( SCOPE_VARFETCH(pp[i],LEVEL=0)) + if LOGICAL_TRUE(defined) then $ + heap_free, ptr_new( SCOPE_VARFETCH(pp[i],LEVEL=0),/no_copy) + + endfor + + return + end + diff --git a/fiasco/tests/idl/ssw_gen_functions/get_uniq.pro b/fiasco/tests/idl/ssw_gen_functions/get_uniq.pro new file mode 100644 index 00000000..982bb2b7 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/get_uniq.pro @@ -0,0 +1,58 @@ +;+ +; Project : HESSI +; +; Name : get_uniq +; +; Purpose : return unique elements of an array +; +; Category : utility +;; +; Syntax : IDL> out=get_uniq(in) +; +; Inputs : IN = array to search +; +; Outputs : OUT = unique elements +; +; Optional Out: SORDER = sorting index +; +; Keywords : NO_CASE: case insensitive ordering on strings +; COUNT: # of uniq values +; EPSILON: positive number ge 0, for gt 0 the difference between +; two consecutive numbers must be gt epsilon for them to be unique. +; +; History : Written 20 Sept 1999, D. Zarro, SM&A/GSFC +; 25-Aug-2006, richard.schwartz@gsfc.nasa.gov; added an epsilon tolerance +; for determining floats to be the same value +; : 16-Sep-2014 - S.Freeland - uniq -> ssw_uniq.pro (avoid +; 8.3/exelis uniq collision) +; : 18-Jul-2018 - return null for non-existent input +; +; Contact : dzarro@solar.stanford.edu +;- + +function get_uniq,array,sorder,no_case=no_case,count=count, epsilon=epsilon + +count=0 +sorder=-1 +if ~exist(array) then return,null() +sorder=0 +if n_elements(array) eq 1 then begin + count=1 + return,array[0] +endif + +sorted=0b +if keyword_set(no_case) then begin + if is_string(array) then begin + sorder=ssw_uniq([strlowcase(array)],sort([strlowcase(array)])) + sorted=1b + endif +endif + +if ~sorted then sorder=ssw_uniq([array],sort([array]), epsilon=epsilon) + +count=n_elements(sorder) +if count eq 1 then sorder=sorder[0] + +return,array[sorder] +end diff --git a/fiasco/tests/idl/ssw_gen_functions/null.pro b/fiasco/tests/idl/ssw_gen_functions/null.pro new file mode 100644 index 00000000..f3ed8f17 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/null.pro @@ -0,0 +1,27 @@ +;+ +; Project : VSO +; +; Name : NULL +; +; Purpose : Return !NULL +; +; Category : Utility +; +; Inputs : None +; +; Outputs : !NULL = '' if !NULL not defined +; +; Keywords : None +; +; History : 9-Dec-2015, Zarro (ADNET) - written +; +; Contact : DZARRO@SOLAR.STANFORD.EDU +;- + +function null + +null='' +defsysv,'!null',exists=i +if i eq 0 then defsysv,'!null','' +return,!null +end diff --git a/fiasco/tests/idl/ssw_gen_functions/repstr.pro b/fiasco/tests/idl/ssw_gen_functions/repstr.pro new file mode 100644 index 00000000..3e1ff9b4 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/repstr.pro @@ -0,0 +1,92 @@ +function repstr,obj,in,out +;+ +; NAME: +; REPSTR +; PURPOSE: +; Replace all occurences of one substring by another. +; EXPLANATION: +; Meant to emulate the string substitution capabilities of text editors +; +; Obsolete since introduction of the REPLACE method for string variables +; introduced in IDL 8.4 +; +; For a more sophisticated routine that allows regular expressions look +; at MG_STRREPLACE() http://docs.idldev.com/idllib/strings/mg_streplace.html +; CALLING SEQUENCE: +; result = repstr( obj, in, out ) +; +; INPUT PARAMETERS: +; obj = object string for editing, scalar or array +; in = substring of 'obj' to be replaced, scalar +; +; OPTIONAL INPUT PARMETER: +; out = what 'in' is replaced with, scalar. If not supplied +; then out = '', i.e. 'in' is not replaced by anything. +; +; OUTPUT PARAMETERS: +; Result returned as function value. Input object string +; not changed unless assignment done in calling program. +; +; PROCEDURE: +; Searches for 'in', splits 'obj' into 3 pieces, reassembles +; with 'out' in place of 'in'. Repeats until all cases done. +; +; EXAMPLE: +; If a = 'I am what I am' then print,repstr(a,'am','was') +; will give 'I was what I was'. +; +; MODIFICATION HISTORY: +; Written by Robert S. Hill, ST Systems Corp., 12 April 1989. +; Accept vector object strings, W. Landsman HSTX, April, 1996 +; Convert loop to LONG, vectorize STRLEN call W. Landsman June 2002 +; Correct bug in optimization, case where STRLEN(OBJ) EQ +; STRLEN(IN), C. Markwardt, Jan 2003 +; Fixed problem when multiple replacements extend the string length +; D. Finkbeiner, W. Landsman April 2003 +; Allow third parameter to be optional again W. Landsman August 2003 +; Remove limitation of 9999 characters, C. Markwardt Dec 2003 +; Test for empty "in" string (causing infinite loop) W. Landsman Jan 2010 +; Streamline code W Landsman Dec 2011 +; Use string .replace method in IDL 8.4 or later W. Landsman Feb 2015 +; Use CALL_METHOD so that it still compiles in IDL 7.1 W.Landsman Aug 2015 +; Keep 3rd parameter optional in V8.4 or later W. Landsman Sep 2016 +; Test for valid parameter values even when using .replace method W.L. Jan 2017 +;- + On_error,2 + compile_opt idl2 + + if N_params() LT 2 then begin + print,'Syntax - result = REPSTR( obj, in, out )' + return, obj + endif + + if N_elements(out) EQ 0 then out = '' + l1 = strlen(in) + if l1 EQ 0 then message,'ERROR - empty input string not allowed' + Nstring = N_elements(obj) + if Nstring EQ 0 then message,'ERROR - undefined object string (first parameter)' + if !VERSION.RELEASE GE '8.4' then return,call_method('replace',obj,in,out) + l2 = strlen(out) + + diflen = l2- l1 + + object = obj + lo = strlen(object) - l1 ;Last character needed to look at + for i= 0L ,Nstring-1 do begin + last_pos = 0 + pos = 0 + while ( pos LE lo[i]) do begin + pos = strpos(object[i],in,last_pos) + if (pos GE 0) then begin + first_part = strmid(object[i],0,pos) + last_part = strmid(object[i],pos+l1) + object[i] = first_part + out + last_part + last_pos = pos + l2 + lo[i] += diflen ;Length of string may have changed + endif else break + endwhile + endfor + + return,object + + end diff --git a/fiasco/tests/idl/ssw_gen_functions/ssw_uniq.pro b/fiasco/tests/idl/ssw_gen_functions/ssw_uniq.pro new file mode 100644 index 00000000..f8830edc --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/ssw_uniq.pro @@ -0,0 +1,118 @@ +;+ +; NAME: +; SSW_UNIQ +; +; PURPOSE: +; Return the subscripts of the unique elements in an array. +; +; Note that repeated elements must be adjacent in order to be +; found. This routine is intended to be used with the SORT +; function. See the discussion of the IDX argument below. +; +; This command is inspired by the Unix uniq(1) command. +; +; CATEGORY: +; Array manipulation. +; +; CALLING SEQUENCE: +; SSW_UNIQ(Array [, Idx] [/first] [EPSILON=epsilon) +; +; INPUTS: +; Array: The array to be scanned. The type and number of dimensions +; of the array are not important. The array must be sorted +; into monotonic order unless the optional parameter Idx is +; supplied. +; +; OPTIONAL INPUT PARAMETERS: +; IDX: This optional parameter is an array of indices into Array +; that order the elements into monotonic order. +; That is, the expression: +; +; Array(Idx) +; +; yields an array in which the elements of Array are +; rearranged into monotonic order. If the array is not +; already in monotonic order, use the command: +; +; SSW_UNIQ(Array, SORT(Array)) +; +; The expression below finds the unique elements of an unsorted +; array: +; +; Array(SSW_UNIQ(Array, SORT(Array))) +; EPSILON: positive number ge 0, for gt 0 the relative difference between +; two consecutive numbers must be gt epsilon for them to be unique. +; +; OUTPUTS: +; An array of indicies into ARRAY is returned. The expression: +; +; ARRAY(SSW_UNIQ(ARRAY)) +; +; will be a copy of the sorted Array with duplicate adjacent +; elements removed. +; +; Optional Keyword Parameter: +; first - if set, return index of FIRST occurence for duplicates +; (default is LAST occurence) +; +; COMMON BLOCKS: +; None. +; +; MODIFICATION HISTORY: +; 29 July 1992, ACY - Corrected for case of all elements the same. +; 30 Aug 1994, SLF - added /first keyword +; 1 Sep 1994, MDM - Modified to return a vector for the case of +; a single element being returned (so it matches +; the pre IDL Ver 3.0 version of UNIQ) +; - Modified to return [0] for a scalar +; 10 Sep 1996, Zarro +; - modified to return 0 for a scalar and a scalar +; for single element being returned. +; 10 Oct 1996, Zarro +; - added OLDWAY keyword to return,[value] for scalar +; value +; 25-Aug-2006, richard.schwartz@gsfc.nasa.gov; added an epsilon tolerance +; for determining floats as the same value +; 15-sep-2014, Freeland - verbatim namepace copy UNIQ -> SSW_UNIQ to avoid 8.3 'uniq' collision +;- + +function SSW_UNIQ, ARRAY, IDX, $ + FIRST=FIRST, OLDWAY=OLDWAY, EPSILON=EPSILON + +; Check the arguments. + default, epsilon, 0.0 + epsilon = abs(epsilon) + isstring = datatype(array,/tname) eq 'STRING' + oldway=keyword_set(oldway) + s = size(ARRAY) + first=keyword_set(first) + + if (s(0) eq 0) then begin + val=0 + if oldway then val=[val] + return,val + endif + + shifts=([-1,1])(first) ;slf - shift direction -> first/last + if n_params() ge 2 then begin ;IDX supplied? + q = array(idx) + if epsilon eq 0 or isstring then $ + indices = where(q ne shift(q,shifts), count) else $ + indices = where(abs(q - shift(q,shifts)) gt abs(q)*epsilon, count) + if (count GT 0) then return, idx(indices) else begin + val=(n_elements(q)-1) * (1-first) + if oldway then val=[val] + return,val + endelse + endif else begin + if epsilon eq 0 or isstring then $ + indices = where(array ne shift(array, shifts), count) else $ + indices = where(abs(array - shift(array,shifts)) gt abs(array)*epsilon, count) + if (count GT 0) then return, indices else begin + val=(n_elements(ARRAY)-1) * (1-first) + if oldway then val=[val] + return,val + endelse + endelse + + end diff --git a/fiasco/tests/idl/ssw_gen_functions/str_index.pro b/fiasco/tests/idl/ssw_gen_functions/str_index.pro new file mode 100644 index 00000000..d3c9b132 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/str_index.pro @@ -0,0 +1,68 @@ +FUNCTION STR_INDEX, str, substr, offset +;+ +; NAME: +; STR_INDEX() +; +; PURPOSE: +; Get indices of a substring (SUBSTR) in string. +; +; EXPLANATION: +; The IDL intrinsic function STRPOS returns only the index of the first +; occurrence of a substring. This routine calls itself recursively to get +; indices of the remaining occurrences. +; +; CALLING SEQUENCE: +; result= STR_INDEX(str, substr [, offset]) +; +; INPUTS: +; STR -- The string in which the substring is searched for +; SUBSTR -- The substring to be searched for within STR +; +; OPTIONAL INPUTS: +; OFFSET -- The character position at which the search is begun. If +; omitted or being negative, the search begins at the first +; character (character position 0). +; +; OUTPUTS: +; RESULT -- Integer scalar or vector containing the indices of SUBSTR +; within STR. If no substring is found, it is -1. +; +; CALLS: +; DELVARX +; +; COMMON BLOCKS: +; STR_INDEX -- internal common block. The variable save in the block is +; deleted upon final exit of this routine. +; +; CATEGORY: +; Utility, string +; +; MODIFICATION HISTORY: +; Written January 3, 1995, Liyun Wang, GSFC/ARC +; Converted to IDL V5.0 W. Landsman September 1997 +; Use size(/TNAME) instead of DATATYPE() W. Landsman October 2001 +; +;- +; + ON_ERROR, 2 + COMMON str_index, idx + + IF N_PARAMS() LT 2 THEN MESSAGE,'Syntax: str_index, str, substr [,offset]' + + IF size(str,/TNAME) NE 'STRING' OR size(substr,/TNAME) NE 'STRING' THEN $ + MESSAGE, 'The first two input parameters must be of string type.' + + IF N_ELEMENTS(offset) EQ 0 THEN pos = 0 ELSE pos = offset + aa = STRPOS(str,substr,pos) + IF aa NE -1 THEN BEGIN + IF N_ELEMENTS(idx) EQ 0 THEN idx = aa ELSE idx = [idx,aa] + bb = str_index(str,substr,aa+1) + RETURN, bb + ENDIF ELSE BEGIN + IF N_ELEMENTS(idx) NE 0 THEN BEGIN + result = idx + delvarx, idx + ENDIF ELSE result = -1 + RETURN, result + ENDELSE +END diff --git a/fiasco/tests/idl/ssw_gen_functions/strpad.pro b/fiasco/tests/idl/ssw_gen_functions/strpad.pro new file mode 100644 index 00000000..f326a879 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/strpad.pro @@ -0,0 +1,102 @@ +;+ +; Project : SOHO - CDS +; +; Name : STRPAD +; +; Purpose : Pads a string with blanks (or whatever) to specified width +; +; +; Explanation : Spaces are added in front of the input string to +; make the returned string have LENGTH characters. +; Use /AFTER to add spaces at the end. +; +; Use : str = strpad(value, length, /after, fill=fill]) +; +; Inputs : VALUE: A string.. +; LENGTH: The desired length of the result in characters +; +; Opt. Inputs : None. +; +; Outputs : Returns the padded string. +; +; Opt. Outputs: None. +; +; Keywords : AFTER : Set to add spaces at the end. +; FILL : The character with which to pad out the string. +; Default is the space character +; +; Restrictions: Value must be a scalar string +; +; Side effects: If the input string is longer than the desired +; width, it is returned without truncation +; +; Category : Utilities, Strings +; +; Written : Stein Vidar Hagfors Haugan, 27 September 1993 +; +; Modified : Corrected typo which stopped /after working. CDP, 28-Sep-94 +; Increased possible length used. CDP, 22-Dec-94 +; Handle arrays of strings. CDP, 16-Mar-95 +; Add FILL keyword and stop overwriting input. CDP, 30-Apr-95 +; Vectorized, richard.schwartz@gsfc.nasa.gov, 23-jan-2003 +; Vectorized even better, Zarro (EER/GSFC), 24-Jan-2003 +; Fixed degenerate dimension bug, Zarro (EER/GSFC), 29-Mar-2003 +;- + + +function strpad, in_txt, length, after=after, fill=fill, no_copy=no_copy + +; +; check basic input +; + +sz=size(in_txt) +if sz[n_elements(sz)-2] ne 7 then return,'' +if exist(fill) then fill=fill else fill = ' ' +if not exist(length) then return,in_txt + +;-- only process strings with length less than new length + +tlen=strlen(in_txt) +mlen=max(tlen) +process=where(tlen lt length,lcount) +if lcount eq 0 then return,in_txt else begin + chk=where(tlen ge length,pcount) + if pcount gt 0 then keep=in_txt[chk] + mlen=max(tlen[process]) +endelse +mlen=mlen > 1 + +;-- convert to byte array + +if keyword_set(no_copy) then byte_in=temporary(in_txt) else byte_in=in_txt + +;-- remove degenerate dimensions + +if sz[0] gt 0 then byte_in=reform(byte_in) + +byte_in = transpose(byte(strmid(temporary(byte_in),0,mlen))) + +;-- pad with 32b blanks + +blank=where(byte_in eq 0b,count) +if count gt 0 then byte_in[blank]=(byte(' '))[0] + +;-- create output byte array + +byte_out = bytarr(n_elements(byte_in[*,0]),length) + (byte(fill))[0] + +if keyword_set(after) then byte_out[0,0]=temporary(byte_in) else $ + byte_out[0,length-mlen]=temporary(byte_in) + +;-- convert back to string + +byte_out=string(transpose(temporary(byte_out))) + +;-- insert back unprocessed strings + +if pcount gt 0 then byte_out[chk]=temporary(keep) + +return,byte_out + +end diff --git a/fiasco/tests/idl/ssw_gen_functions/tag_exist.pro b/fiasco/tests/idl/ssw_gen_functions/tag_exist.pro new file mode 100644 index 00000000..8006edcc --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/tag_exist.pro @@ -0,0 +1,99 @@ +;+ +; NAME: +; TAG_EXIST() +; PURPOSE: +; To test whether a tag name exists in a structure. +; EXPLANATION: +; Routine obtains a list of tagnames and tests whether the requested one +; exists or not. The search is recursive so if any tag names in the +; structure are themselves structures the search drops down to that level. +; (However, see the keyword TOP_LEVEL). +; +; CALLING SEQUENCE: +; status = TAG_EXIST(str, tag, [ INDEX =, /TOP_LEVEL, /QUIET ] ) +; +; INPUT PARAMETERS: +; str - structure variable to search +; tag - tag name to search for, scalar string +; +; OUTPUTS: +; Function returns 1b if tag name exists or 0b if it does not. +; +; OPTIONAL INPUT KEYWORD: +; /TOP_LEVEL = If set, then only the top level of the structure is +; searched. +; /QUIET - if set, then do not print messages if invalid parameters given +; /RECURSE - does nothing but kept for compatibility with the +; Solarsoft version for which recursion is not the default +; http://sohowww.nascom.nasa.gov/solarsoft/gen/idl/struct/tag_exist.pro +; OPTIONAL OUTPUT KEYWORD: +; INDEX = index of matching tag, scalar longward, -1 if tag name does +; not exist +; +; EXAMPLE: +; Determine if the tag 'THICK' is in the !P system variable +; +; IDL> print,tag_exist(!P,'THICK') +; +; PROCEDURE CALLS: +; None. +; +; MODIFICATION HISTORY: : +; Written, C D Pike, RAL, 18-May-94 +; Passed out index of matching tag, D Zarro, ARC/GSFC, 27-Jan-95 +; William Thompson, GSFC, 6 March 1996 Added keyword TOP_LEVEL +; Zarro, GSFC, 1 August 1996 Added call to help +; Use SIZE(/TNAME) rather than DATATYPE() W. Landsman October 2001 +; Added /RECURSE and /QUIET for compatibility with Solarsoft version +; W. Landsman March 2009 +; Slightly faster algorithm W. Landsman July 2009 +; July 2009 update was not setting Index keyword W. L Sep 2009. +; Use V6.0 notation W.L. Jan 2012 +; Not setting index again, sigh W.L./ K. Allers Jan 2012 +;- + +function tag_exist, str, tag,index=index, top_level=top_level,recurse=recurse, $ + quiet=quiet + +; +; check quantity of input +; +compile_opt idl2 +if N_params() lt 2 then begin + print,'Use: status = tag_exist(structure, tag_name)' + return,0b +endif + +; +; check quality of input +; + +if size(str,/TNAME) ne 'STRUCT' or size(tag,/TNAME) ne 'STRING' then begin + if ~keyword_set(quiet) then begin + if size(str,/TNAME) ne 'STRUCT' then help,str + if size(tag,/TNAME) ne 'STRING' then help,tag + print,'Use: status = tag_exist(str, tag)' + print,'str = structure variable' + print,'tag = string variable' + endif + return,0b +endif + + tn = tag_names(str) + + index = where(tn eq strupcase(tag), nmatch) + + if ~nmatch && ~keyword_set(top_level) then begin + status= 0b + for i=0,n_elements(tn)-1 do begin + if size(str.(i),/TNAME) eq 'STRUCT' then $ + status=tag_exist(str.(i),tag,index=index) + if status then return,1b + endfor + return,0b + +endif else begin + index = index[0] + return,logical_true(nmatch) + endelse +end diff --git a/fiasco/tests/idl/ssw_gen_functions/valid_num.pro b/fiasco/tests/idl/ssw_gen_functions/valid_num.pro new file mode 100644 index 00000000..05b2a205 --- /dev/null +++ b/fiasco/tests/idl/ssw_gen_functions/valid_num.pro @@ -0,0 +1,80 @@ +;+ +; NAME: +; VALID_NUM() +; PURPOSE: +; Check if a string is a valid number representation. +; EXPLANATION: +; The input string is parsed for characters that may possibly +; form a valid number. It is more robust than simply checking +; for an IDL conversion error because that allows strings such +; as '22.3qwert' to be returned as the valid number 22.3 +; +; This function had a major rewrite in August 2008 to use STREGEX +; and allow vector input. It should be backwards compatible. +; CALLING SEQUENCE: +; IDL> status = valid_num(string [,value] [,/integer]) +; +; INPUTS: +; string - the string to be tested, scalar or array +; +; RETURNS +; status - byte scalar or array, same size as the input string +; set to 1 where the string is a valid number, 0 for invalid +; OPTIONAL OUTPUT: +; value - The value the string decodes to, same size as input string. +; This will be returned as a double precision number unless +; /INTEGER is present, in which case a long integer is returned. +; +; OPTIONAL INPUT KEYWORD: +; /INTEGER - if present code checks specifically for an integer. +; EXAMPLES: +; (1) IDL> print,valid_num(3.2,/integer) +; --> 0 ;Since 3.2 is not an integer +; (2) IDL> str =['-0.03','2.3g', '3.2e12'] +; IDL> test = valid_num(str,val) +; test = [1,0,1] & val = [-0.030000000 ,NaN ,3.2000000e+12] +; REVISION HISTORY: +; Version 1, C D Pike, RAL, 24-May-93 +; Version 2, William Thompson, GSFC, 14 October 1994 +; Added optional output parameter VALUE to allow +; VALID_NUM to replace STRNUMBER in FITS routines. +; Version 3 Wayne Landsman rewrite to use STREGEX, vectorize +; Version 4 W.L. (fix from C. Markwardt) Better Stregex expression, +; was missing numbers like '134.' before Jan 1 2010 +;- + +FUNCTION valid_num, string, value, INTEGER=integer + On_error,2 + compile_opt idl2 + +; A derivation of the regular expressions below can be found on +; http://wiki.tcl.tk/989 + + if keyword_set(INTEGER) then $ + st = '^[-+]?[0-9][0-9]*$' else $ ;Integer + st = '^[-+]?([0-9]+\.?[0-9]*|\.[0-9]+)([eEdD][-+]?[0-9]+)?$' ;F.P. + +;Simple return if we just need a boolean test. + if N_params() EQ 1 then return, stregex(strtrim(string,2),st,/boolean) + + + vv = stregex(strtrim(string,2),st,/boolean) + if size(string,/N_dimen) EQ 0 then begin ;Scalar + if vv then $ + value= keyword_set(integer) ? long(string) : double(string) + endif else begin ;Array + + g = where(vv,Ng) + if Ng GT 0 then begin ;Need to create output vector + if keyword_set(integer) then begin + value = vv*0L + value[g] = long(string[g]) + endif else begin + value = replicate(!VALUES.D_NAN,N_elements(vv)) + value[g] = double(string[g]) + endelse + endif + endelse + + return,vv + end diff --git a/fiasco/tests/idl/test_idl_continuum.py b/fiasco/tests/idl/test_idl_continuum.py index b2b353dd..1305bb80 100644 --- a/fiasco/tests/idl/test_idl_continuum.py +++ b/fiasco/tests/idl/test_idl_continuum.py @@ -7,6 +7,7 @@ import fiasco +from fiasco.tests.idl.helpers import run_idl_script from fiasco.util.exceptions import MissingDatasetException @@ -30,110 +31,113 @@ def wavelength(): @pytest.fixture -def idl_input_args(all_ions, wavelength, ascii_dbase_root): - abundance_name = all_ions[0]._dset_names['abundance_filename'] - ioneq_name = all_ions[0]._dset_names['ioneq_filename'] +def idl_input_args(all_ions, wavelength): return { 'wavelength': wavelength, 'temperature': all_ions.temperature, - 'abundance_filename': ascii_dbase_root / 'abundance' / f'{abundance_name}.abund', - 'ioneq_filename': ascii_dbase_root / 'ioneq' / f'{ioneq_name}.ioneq', + 'abundance': all_ions[0]._dset_names['abundance_filename'], + 'ioneq': all_ions[0]._dset_names['ioneq_filename'], } -def test_idl_compare_free_free(idl_env, all_ions, wavelength, idl_input_args): - ff_python = all_ions.free_free(wavelength).to_value('erg cm3 s-1 Angstrom-1') - # Run IDL free-free calculation +def test_idl_compare_free_free(idl_env, all_ions, idl_input_args, dbase_version): script = """ ; set common block common elements, abund, abund_ref, ioneq, ioneq_logt, ioneq_ref ; read abundance and ionization equilibrium - abundfile='{{ abundance_filename }}' - read_abund, abundfile, abund, abund_ref - ioneqfile="{{ ioneq_filename }}" - read_ioneq, ioneqfile, ioneq_logt, ioneq, ioneq_ref + abund_file = FILEPATH('{{abundance}}.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance') + ioneq_file = FILEPATH('{{ioneq}}.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq') + read_abund, abund_file, abund, abund_ref + read_ioneq, ioneq_file, ioneq_logt, ioneq, ioneq_ref ; set temperature and wavelength temperature = {{ temperature | to_unit('K') | force_double_precision }} wavelength = {{ wavelength | to_unit('Angstrom') | force_double_precision }} ; calculate free-free - freefree, temperature, wavelength, ff, /no_setup - - ; The output of freefree is scaled by 10^40 - ff = ff/1d40 + freefree, temperature, wavelength, free_free, /no_setup """ - res_idl = idl_env.run(script, args=idl_input_args, verbose=True) - ff_idl = res_idl['ff'] + idl_result = run_idl_script(idl_env, + script, + idl_input_args, + ['free_free'], + 'freefree_all_ions', + dbase_version, + format_func={'free_free': lambda x: x/1e40*u.Unit('erg cm3 s-1 Angstrom-1')}) + + free_free_python = all_ions.free_free(idl_result['wavelength']) # Compare IDL and Python calculation - assert u.allclose(ff_idl, ff_python, atol=0.0, rtol=0.005) + assert u.allclose(idl_result['free_free'], free_free_python, atol=None, rtol=0.005) -def test_idl_compare_free_bound(idl_env, all_ions, wavelength, idl_input_args): - fb_python = all_ions.free_bound(wavelength).to_value('erg cm3 s-1 Angstrom-1') - # NOTE: our expression does not include the 1/4π per steradian - fb_python /= 4*np.pi - # Run IDL free-free calculation +def test_idl_compare_free_bound(idl_env, all_ions, idl_input_args, dbase_version): script = """ ; set common block common elements, abund, abund_ref, ioneq, ioneq_logt, ioneq_ref ; read abundance and ionization equilibrium - abundfile='{{ abundance_filename }}' - read_abund, abundfile, abund, abund_ref - ioneqfile="{{ ioneq_filename }}" - read_ioneq, ioneqfile, ioneq_logt, ioneq, ioneq_ref + abund_file = FILEPATH('{{abundance}}.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance') + ioneq_file = FILEPATH('{{ioneq}}.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq') + read_abund, abund_file, abund, abund_ref + read_ioneq, ioneq_file, ioneq_logt, ioneq, ioneq_ref ; set temperature and wavelength temperature = {{ temperature | to_unit('K') | force_double_precision }} wavelength = {{ wavelength | to_unit('Angstrom') | force_double_precision }} ; calculate free-bound - freebound, temperature, wavelength, fb, /no_setup - - ; The output of freefree is scaled by 10^40 - fb = fb/1d40 + freebound, temperature, wavelength, free_bound, /no_setup """ - res_idl = idl_env.run(script, args=idl_input_args, verbose=True) - fb_idl = res_idl['fb'] + idl_result = run_idl_script(idl_env, + script, + idl_input_args, + ['free_bound'], + 'freebound_all_ions', + dbase_version, + format_func={'free_bound': lambda x: x/1e40*u.Unit('erg cm3 s-1 Angstrom-1')}) + free_bound_python = all_ions.free_bound(idl_result['wavelength']) + # NOTE: our expression does not include the 1/4π per steradian + free_bound_python /= 4*np.pi # Compare IDL and Python calculation - assert u.allclose(fb_idl, fb_python, atol=0.0, rtol=0.005) + assert u.allclose(idl_result['free_bound'], free_bound_python, atol=None, rtol=0.005) -def test_idl_compare_free_bound_ion(idl_env, all_ions, wavelength, idl_input_args): +def test_idl_compare_free_bound_ion(idl_env, all_ions, idl_input_args, dbase_version): script = """ ; set common block common elements, abund, abund_ref, ioneq, ioneq_logt, ioneq_ref ; read abundance and ionization equilibrium - abundfile='{{ abundance_filename }}' - read_abund, abundfile, abund, abund_ref - ioneqfile="{{ ioneq_filename }}" - read_ioneq, ioneqfile, ioneq_logt, ioneq, ioneq_ref + abund_file = FILEPATH('{{abundance}}.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance') + ioneq_file = FILEPATH('{{ioneq}}.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq') + read_abund, abund_file, abund, abund_ref + read_ioneq, ioneq_file, ioneq_logt, ioneq, ioneq_ref ; set temperature and wavelength temperature = {{ temperature | to_unit('K') | force_double_precision }} wavelength = {{ wavelength | to_unit('Angstrom') | force_double_precision }} ; calculate free-bound - freebound_ion, temperature, wavelength, fb, {{ atomic_number }}, {{ ionization_stage }} - - ; The output of freefree is scaled by 10^40 - fb = fb/1d40 + freebound_ion, temperature, wavelength, free_bound, {{ atomic_number }}, {{ ionization_stage }} """ # NOTE: this should be something we parametrize over such that there is a test for each # ion rather than all being lumped into a single test that takes a really long time for ion in all_ions: try: - fb_python = ion.free_bound(wavelength) + free_bound_python = ion.free_bound(idl_input_args['wavelength']) except MissingDatasetException: continue - fb_python = fb_python.to_value('erg cm3 s-1 Angstrom-1') # NOTE: our expression does not include the 1/4π per steradian - fb_python /= 4*np.pi + free_bound_python /= 4*np.pi args = {**idl_input_args, 'atomic_number':ion.atomic_number, 'ionization_stage':ion.ionization_stage} - res_idl = idl_env.run(script, args=args, verbose=True) - fb_idl = res_idl['fb'] + idl_result = run_idl_script(idl_env, + script, + args, + ['free_bound'], + f'freebound_{ion.atomic_number}_{ion.ionization_stage}', + dbase_version, + format_func={'free_bound': lambda x: x/1e40*u.Unit('erg cm3 s-1 Angstrom-1')}, + write_file=False) # Compare IDL and Python calculation - assert u.allclose(fb_idl, fb_python, atol=0.0, rtol=0.006) + assert u.allclose(idl_result['free_bound'], free_bound_python, atol=None, rtol=0.006) diff --git a/fiasco/tests/idl/test_idl_goft.py b/fiasco/tests/idl/test_idl_goft.py new file mode 100644 index 00000000..dac7404c --- /dev/null +++ b/fiasco/tests/idl/test_idl_goft.py @@ -0,0 +1,88 @@ +""" +IDL comparison tests for a few representative contribution functions. +""" +import astropy.units as u +import numpy as np +import pytest + +import fiasco + +from fiasco.tests.idl.helpers import run_idl_script +from fiasco.util import parse_ion_name + +# NOTE: This is necessary because I cannot figure out how to select the contribution function +# by wavelength so I have to run the g_of_t function once with the GUI selector to work out +# what integer index corresponds to which wavelength. For any additional test that is added to +# the list below, this index will need to be computed and added to the list below. +INDEX_WAVE_MAPPING = { + 200.972*u.Angstrom: 297, + 171.073*u.Angstrom: 13946, + 188.497*u.Angstrom: 22527, + 197.862*u.Angstrom: 27964, + 262.984*u.Angstrom: 1415, +} + + +@pytest.mark.parametrize(('ion_name', 'wavelength'), [ + ('Ca XV', 200.972*u.Angstrom), + ('Fe IX', 171.073*u.Angstrom), + ('Fe XI', 188.497*u.Angstrom), + ('Fe XIV', 197.862*u.Angstrom), + ('Fe XVI', 262.984*u.Angstrom), +]) +def test_idl_compare_goft(idl_env, hdf5_dbase_root, dbase_version, ion_name, wavelength): + goft_script = """ + abund_file = FILEPATH('{{abundance}}.abund', ROOT_DIR=!xuvtop, SUBDIR='abundance') + ioneq_file = FILEPATH('{{ioneq}}.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq') + density = {{ density | to_unit('cm-3') | log10 | force_double_precision }} + wave_min = {{ (wavelength - wave_window) | to_unit('angstrom') | force_double_precision }} + wave_max = {{ (wavelength + wave_window) | to_unit('angstrom') | force_double_precision }} + contribution_function = g_of_t({{ Z }},$ + {{ iz }},$ + dens=density,$ + abund_file=abund_file,$ + ioneq_file=ioneq_file,$ + {% if index %}index={{ index }},/quiet,${% endif %} + wrange=[wave_min, wave_max]) + ; Call this function to get the temperature array + read_ioneq,ioneq_file,temperature,ioneq,ref + """ + # Setup IDl arguments + Z, iz = parse_ion_name(ion_name) + input_args = { + 'Z': Z, + 'iz': iz, + 'wavelength': wavelength, + 'wave_window': 1 * u.angstrom, + 'index': INDEX_WAVE_MAPPING[wavelength], + 'density': 1e+10 * u.cm**(-3), + 'abundance': 'sun_coronal_1992_feldman_ext', + 'ioneq': 'chianti', + } + formatters = {'temperature': lambda x: 10**x*u.K, + 'contribution_function': lambda x: x*u.Unit('erg cm3 s-1')} + idl_result = run_idl_script(idl_env, + goft_script, + input_args, + ['temperature', 'contribution_function'], + f'goft_{Z}_{iz}_{wavelength.to_value("AA"):.3f}', + dbase_version, + format_func=formatters) + # Run equivalent fiasco code + ion = fiasco.Ion(ion_name, + idl_result['temperature'], + hdf5_dbase_root=hdf5_dbase_root, + abundance_filename=idl_result['abundance'], + ioneq_filename=idl_result['ioneq']) + contribution_func = ion.contribution_function(idl_result['density']) + idx = np.argmin(np.abs(ion.transitions.wavelength[~ion.transitions.is_twophoton] - idl_result['wavelength'])) + goft_python = contribution_func[:, 0, idx] + # Find relevant range for comparison. The solutions may diverge many orders of magnitude below + # the peak of the contribution function, but that is not relevant in assessing meaningful + # differences between the IDL and Python approaches. Thus, we only assess the differences + # where the contribution function is above some threshold relative to the peak of the + # contribution function. + goft_idl = idl_result['contribution_function'] + i_compare = np.where(goft_idl>=goft_idl.max()*1e-10) + # Compare results + assert u.allclose(goft_idl[i_compare], goft_python[i_compare], atol=None, rtol=0.05) diff --git a/fiasco/tests/idl/test_idl_ioneq.py b/fiasco/tests/idl/test_idl_ioneq.py index 8085f2c3..eb82e115 100644 --- a/fiasco/tests/idl/test_idl_ioneq.py +++ b/fiasco/tests/idl/test_idl_ioneq.py @@ -2,23 +2,12 @@ IDL comparison tests for ionization equilibria """ import astropy.units as u -import pathlib import pytest import fiasco - -@pytest.fixture -def ioneq_from_idl(idl_env, ascii_dbase_root): - script = """ - ioneqfile="{{ ioneq_filename }}" - read_ioneq, ioneqfile, ioneq_logt, ioneq, ioneq_ref - """ - args = { - 'ioneq_filename': ascii_dbase_root / 'ioneq' / 'chianti.ioneq', - } - res_idl = idl_env.run(script, args=args, verbose=True) - return res_idl +from fiasco.tests.idl.helpers import run_idl_script +from fiasco.util import parse_ion_name @pytest.mark.parametrize('ion_name', [ @@ -33,13 +22,24 @@ def ioneq_from_idl(idl_env, ascii_dbase_root): 'Ca 2', 'Fe 20', ]) -def test_ioneq_from_idl(ion_name, ioneq_from_idl, hdf5_dbase_root): - temperature = 10**ioneq_from_idl['ioneq_logt'] * u.K - ion_kwargs = { - 'ioneq_filename': pathlib.Path(str(ioneq_from_idl['ioneqfile'])).stem, - 'hdf5_dbase_root': hdf5_dbase_root, - } - ion = fiasco.Ion(ion_name, temperature, **ion_kwargs) - ioneq_idl = ioneq_from_idl['ioneq'][ion.charge_state, ion.atomic_number-1, :] - ioneq_python = ion.ioneq - assert u.allclose(ioneq_idl, ioneq_python, rtol=0.0, atol=1e-5) +def test_ioneq_from_idl(ion_name, idl_env, dbase_version, hdf5_dbase_root): + Z, iz = parse_ion_name(ion_name) + script = """ + ioneq_file = FILEPATH('{{ioneq_filename}}.ioneq', ROOT_DIR=!xuvtop, SUBDIR='ioneq') + read_ioneq, ioneq_file, temperature, ioneq, ioneq_ref + ioneq = ioneq[*,{{Z-1}},{{iz-1}}] + """ + formatters = {'temperature': lambda x: 10**x*u.K, + 'ioneq': lambda x: x*u.dimensionless_unscaled} + idl_result = run_idl_script(idl_env, + script, + {'ioneq_filename': 'chianti', 'Z': Z, 'iz': iz}, + ['temperature', 'ioneq'], + f'ioneq_{Z}_{iz}', + dbase_version, + format_func=formatters) + ion = fiasco.Ion(ion_name, + idl_result['temperature'], + hdf5_dbase_root=hdf5_dbase_root, + ioneq_filename=idl_result['ioneq_filename']) + assert u.allclose(idl_result['ioneq'], ion.ioneq, rtol=0.0, atol=1e-5) diff --git a/fiasco/tests/test_ion.py b/fiasco/tests/test_ion.py index 13c5c8ae..bfa16e97 100644 --- a/fiasco/tests/test_ion.py +++ b/fiasco/tests/test_ion.py @@ -244,7 +244,7 @@ def test_level_populations_normalized(pops_no_correction, pops_with_correction): assert u.allclose(pops_no_correction.sum(axis=1), 1, atol=None, rtol=1e-15) -@pytest.mark.requires_dbase_version('<=8') +@pytest.mark.requires_dbase_version('<=','8.0.7') def test_level_populations_correction(fe20, pops_no_correction, pops_with_correction): # Test level-resolved correction applied to correct levels i_corrected = np.unique(np.concatenate([fe20._cilvl['upper_level'], fe20._reclvl['upper_level']])) diff --git a/fiasco/util/data/file_hashes_v8.0.7.json b/fiasco/util/data/file_hashes_v8.0.7.json new file mode 100644 index 00000000..840ccd65 --- /dev/null +++ b/fiasco/util/data/file_hashes_v8.0.7.json @@ -0,0 +1 @@ +{"sc_sc_2_sc_2.easplups": "83f0520ca09fbd55155fc5f04a268623", "sc_sc_2_sc_2.diparams": "764e2c96c30abf960d47df58a420e4e0", "sc_sc_2_sc_2.drparams": "bf9e51efa5dd5a7594ff67a75730c2eb", "sc_sc_2_sc_2.rrparams": "60581cbe8a90de12e4d11bad0f0107c1", "sc_sc_2_sc_2.easplom": "afc18dd0441f6e24dec26864f53b8fed", "sc_sc_5_sc_5.rrparams": "1638a03d17c5dbc67c3f4c11648a4c6f", "sc_sc_5_sc_5.drparams": "1c79851e56a9a45a888df3663e466091", "sc_sc_5_sc_5.diparams": "a3ca232864b6ca92a8ae2811202cc4a9", "sc_sc_5_sc_5.easplom": 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"dem_version_3_prominence.dem": "2e79e8123a0e543d5f4194afa763237c", "dem_version_3_coronal_hole.dem": "3c4bfd41f7ede044f52b1711dd009f2f", "dem_version_3_quiet_sun_cds_meyer.dem": "ef9daf69bfd0a502345c4a80da2aa568", "dem_version_3_quiet_sun_cds.dem": "32e39f4503fdb50002a98b4247473893", "dem_version_3_active_region.dem": "942b4492a6bba9679fe7e895469670fc"} \ No newline at end of file diff --git a/fiasco/util/setup_db.py b/fiasco/util/setup_db.py index 7cc9cfef..f0b846b6 100644 --- a/fiasco/util/setup_db.py +++ b/fiasco/util/setup_db.py @@ -3,19 +3,19 @@ """ import h5py import hashlib +import json import numpy as np import pathlib import tarfile from astropy.config import set_temp_cache from astropy.utils.console import ProgressBar -from astropy.utils.data import download_file +from astropy.utils.data import download_file, get_pkg_data_path import fiasco.io -from fiasco.io import DataIndexer from fiasco.util.exceptions import MissingASCIIFileError, UnsupportedVersionError -from fiasco.util.util import get_chianti_catalog, query_yes_no +from fiasco.util.util import get_chianti_catalog, query_yes_no, read_chianti_version FIASCO_HOME = pathlib.Path.home() / '.fiasco' CHIANTI_URL = 'http://download.chiantidatabase.org/CHIANTI_v{version}_database.tar.gz' @@ -81,21 +81,21 @@ def check_database(hdf5_dbase_root, **kwargs): # FIXME: how to gracefully handle this exit? return None download_dbase(ascii_dbase_url, ascii_dbase_root) - # If we made it this far, build the HDF5 database - files = kwargs.get('files') - build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=files) # Ensure that an unsupported version is not being passed to fiasco # NOTE: this check is only meant to be bypassed when testing new # versions. Hence, this kwarg is not documented if kwargs.get('check_chianti_version', True): - check_database_version(hdf5_dbase_root) + check_database_version(ascii_dbase_root) + # If we made it this far, build the HDF5 database + files = kwargs.get('files') + build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=files, check_hash=kwargs.get('check_hash', False)) -def check_database_version(hdf5_dbase_root): - dl = DataIndexer.create_indexer(hdf5_dbase_root, '/h/h_1/elvlc') - if dl.version not in SUPPORTED_VERSIONS: +def check_database_version(ascii_dbase_root): + version = read_chianti_version(ascii_dbase_root) + if str(version) not in SUPPORTED_VERSIONS: raise UnsupportedVersionError( - f'CHIANTI {dl.version} is not in the list of supported versions {SUPPORTED_VERSIONS}.') + f'CHIANTI {version} is not in the list of supported versions {SUPPORTED_VERSIONS}.') def download_dbase(ascii_dbase_url, ascii_dbase_root): @@ -120,7 +120,24 @@ def md5hash(path): return hashlib.md5(f.read()).hexdigest() -def build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=None): +def _get_hash_table(version): + data_dir = pathlib.Path(get_pkg_data_path('data', package='fiasco.util')) + file_path = data_dir / f'file_hashes_v{version}.json' + with open(file_path) as f: + hash_table = json.load(f) + return hash_table + + +def _check_hash(parser, hash_table): + actual = md5hash(parser.full_path) + key = '_'.join(parser.full_path.relative_to(parser.ascii_dbase_root).parts) + if hash_table[key] != actual: + raise RuntimeError( + f'Hash of {parser.full_path} ({actual}) did not match expected hash ({hash_table[key]})' + ) + + +def build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=None, check_hash=False): """ Assemble HDF5 file from raw ASCII CHIANTI database. @@ -132,10 +149,10 @@ def build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=None): Path to HDF5 file files : `list` or `dict`, optional A list of files to update in the HDF5 database. By default, - this is all of the files in `ascii_dbase_root`. If a `dict`, the - dictionary keys must contain filenames and the items corresponding - expected md5 hash of the file. Building the database will fail if any - of the md5 hashes is not as expected. + this is all of the files in `ascii_dbase_root`. + check_hash: `bool`, optional + If True, check the file hash before adding it to the database. + Building the database will fail if any of the hashes is not as expected. """ # Import the logger here to avoid circular imports from fiasco import log @@ -146,21 +163,25 @@ def build_hdf5_dbase(ascii_dbase_root, hdf5_dbase_root, files=None): tmp = get_chianti_catalog(ascii_dbase_root) for k in tmp: files += tmp[k] + if check_hash: + version = read_chianti_version(ascii_dbase_root) + hash_table = _get_hash_table(version) + log.debug(f'Checking hashes for version {version}') log.debug(f'Building HDF5 database in {hdf5_dbase_root}') with ProgressBar(len(files)) as progress: with h5py.File(hdf5_dbase_root, 'a') as hf: for f in files: parser = fiasco.io.Parser(f, ascii_dbase_root=ascii_dbase_root) - if isinstance(files, dict): - expected = files[f] - actual = md5hash(parser.full_path) - if expected != actual: - raise RuntimeError(f'Hash of {parser.full_path} ({actual}) did not match expected hash ({expected})') try: df = parser.parse() except MissingASCIIFileError as e: log.debug(f'{e}. Not including {f} in {hdf5_dbase_root}') else: + # NOTE: This conditional is purposefully placed here because files that fail to parse + # do not have a valid full path and thus their hash cannot be checked. When the parsing + # is eventually simplified, this can be moved to a more sane place. + if check_hash: + _check_hash(parser, hash_table) parser.to_hdf5(hf, df) progress.update() # Build an index for quick lookup of all ions in database diff --git a/fiasco/util/tests/test_util.py b/fiasco/util/tests/test_util.py index 56a9afd9..5ffbd01c 100644 --- a/fiasco/util/tests/test_util.py +++ b/fiasco/util/tests/test_util.py @@ -1,6 +1,7 @@ """ Tests for util functions """ +import packaging.version import pytest from fiasco.util import get_chianti_catalog, parse_ion_name, read_chianti_version @@ -39,7 +40,4 @@ def test_get_chianti_catalog(ascii_dbase_root): def test_chianti_version(ascii_dbase_root): version = read_chianti_version(ascii_dbase_root) - assert isinstance(version, dict) - for k in ['major', 'minor', 'patch']: - assert k in version - assert isinstance(version[k], int) + assert isinstance(version, packaging.version.Version) diff --git a/fiasco/util/util.py b/fiasco/util/util.py index 57a69908..d96ece20 100644 --- a/fiasco/util/util.py +++ b/fiasco/util/util.py @@ -7,6 +7,7 @@ import plasmapy.particles import sys +from packaging.version import Version from plasmapy.utils import roman FIASCO_HOME = pathlib.Path.home() / '.fiasco' @@ -120,23 +121,20 @@ def walk_sub_dir(subdir): def read_chianti_version(ascii_dbase_root): """ Read the CHIANTI version number from the ASCII database. + + Parameters + ---------- + asciii_dbase_root: `str` or `pathlib.Path` + + Returns + ------- + : `packaging.version.Version` """ version_file = pathlib.Path(ascii_dbase_root) / 'VERSION' with version_file.open() as f: lines = f.readlines() - version = lines[0].strip().split('.') - version_dict = {'major': 0, 'minor': 0, 'patch': 0} - n = len(version) - if n > 0: - version_dict['major'] = int(version[0]) - if n > 1: - version_dict['minor'] = int(version[1]) - if n > 2: - version_dict['patch'] = int(version[2]) - if n > 3: - import fiasco - fiasco.log.warning(f'Version {version} has an unexpected number of entries.') - return version_dict + version = lines[0].strip() + return Version(version) def query_yes_no(question, default="yes"): diff --git a/pyproject.toml b/pyproject.toml index f26178a7..95eaf77c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,14 +54,20 @@ Issues = "https://github.com/wtbarnes/fiasco/issues/" all = ["fiasco"] test = [ "fiasco[all]", + "asdf", + "asdf-astropy", "pytest", "pytest-astropy", "pytest-cov", "matplotlib", ] +test_idl = [ + "fiasco[test]", + "hissw", +] docs =[ "fiasco[all]", - "sphinx>=4.2,<5", + "sphinx>=4.2", "sphinx-automodapi", "sphinx-gallery", "towncrier", @@ -88,22 +94,14 @@ remote_data_strict = "False" filterwarnings =[ "error", "ignore:numpy.ndarray size changed", + "ignore:The unit 'erg' has been deprecated in the VOUnit standard.*:astropy.units.core.UnitsWarning", + "ignore:The unit 'Angstrom' has been deprecated in the VOUnit standard.*:astropy.units.core.UnitsWarning", ] [tool.coverage.run] +branch = true omit = [ - "fiasco/conftest.py", - "fiasco/*setup_package*", - "fiasco/tests/*", - "fiasco/*/tests/*", - "fiasco/extern/*", - "fiasco/version*", - "*/fiasco/conftest.py", - "*/fiasco/*setup_package*", - "*/fiasco/tests/*", - "*/fiasco/*/tests/*", - "*/fiasco/extern/*", - "*/fiasco/version*", + "*/test_idl*.py" ] [tool.coverage.report] @@ -122,7 +120,7 @@ honor_noqa = true lines_between_types = 1 [tool.codespell] -skip = "*.fts,*.fits,venv,*.pro,*.bib" +skip = "*.fts,*.fits,venv,*.pro,*.bib,*.asdf,*.json" ignore-words-list = "te,emiss" [tool.ruff] diff --git a/tools/generate_hash_table.py b/tools/generate_hash_table.py new file mode 100644 index 00000000..778c86ef --- /dev/null +++ b/tools/generate_hash_table.py @@ -0,0 +1,47 @@ +""" +Script for generating hash table for all files in the CHIANTI database +""" +import click +import json +import pathlib + +from astropy.utils.data import get_pkg_data_path +from itertools import chain + +from fiasco.util.setup_db import md5hash +from fiasco.util.util import get_chianti_catalog, read_chianti_version + + +def build_ion_path(name): + id = name.split('.')[0].split('_') + return pathlib.Path(id[0]) / f'{id[0]}_{id[1]}' / name + + +def build_hash_table(dbase_root): + dbase_root = pathlib.Path(dbase_root) + catalogue = get_chianti_catalog(dbase_root) + filepaths = chain( + map(build_ion_path, catalogue['ion_files']), + map(lambda x: pathlib.Path('abundance') / x, catalogue['abundance_files']), + map(lambda x: pathlib.Path('ioneq') / x, catalogue['ioneq_files']), + map(lambda x: pathlib.Path('ip') / x, catalogue['ip_files']), + map(lambda x: pathlib.Path('continuum') / x, catalogue['continuum_files']), + map(lambda x: pathlib.Path('dem') / x, catalogue['dem_files']), + ) + filepaths = map(lambda x: dbase_root / x, filepaths) + return {'_'.join(f.relative_to(dbase_root).parts): md5hash(f) for f in filepaths} + + +@click.command() +@click.option('--database', required=True, type=str) +def write_hash_table(database): + data_dir = pathlib.Path(get_pkg_data_path('data', package='fiasco.util')) + dbase_version = read_chianti_version(database) + file_path = data_dir / f'file_hashes_v{dbase_version}.json' + hash_table = build_hash_table(database) + with open(file_path, 'w') as f: + json.dump(hash_table, f) + + +if __name__ == '__main__': + write_hash_table()