From a81c4d4b90e2932dcf5cdba30c5ea6525fe32245 Mon Sep 17 00:00:00 2001
From: rraadd88 <rohanadandage@gmail.com>
Date: Thu, 23 Nov 2023 18:24:56 -0500
Subject: [PATCH] updates

---
 .gitignore                                     |  7 +++++++
 CITATION.cff                                   |  2 +-
 examples/io_read_nd2.ipynb                     |  3 ++-
 .../protein_abundance_by_marker_location.ipynb | 18 ++++++++++++++++++
 htsimaging/viz/image.py                        |  6 ++++++
 setup.py                                       |  5 +++--
 6 files changed, 37 insertions(+), 4 deletions(-)

diff --git a/.gitignore b/.gitignore
index ed5c5ca..322472c 100755
--- a/.gitignore
+++ b/.gitignore
@@ -78,3 +78,10 @@ target/
 
 6
 *.bak
+examples/*/*
+examples/*.npy
+examples/*test*
+examples/_*
+examples/_*/
+_*/
+examples/*demo_data*
diff --git a/CITATION.cff b/CITATION.cff
index 2ac2af3..08c390d 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -15,4 +15,4 @@ identifiers:
     value: 10.5281/zenodo.8264035
 repository-code: 'https://github.com/rraadd88/htsimaging'
 version: 1.0.4
-date-released: '2023-08-10'
\ No newline at end of file
+date-released: '2023-08-10'
diff --git a/examples/io_read_nd2.ipynb b/examples/io_read_nd2.ipynb
index f69fee9..5c8aa1c 100755
--- a/examples/io_read_nd2.ipynb
+++ b/examples/io_read_nd2.ipynb
@@ -25,7 +25,8 @@
     "from os.path import dirname,splitext\n",
     "from os import makedirs\n",
     "\n",
-    "import nd2\n",
+    "#!pip install nd2\n",
+    "import nd2 \n",
     "import numpy as np"
    ]
   },
diff --git a/examples/protein_abundance_by_marker_location.ipynb b/examples/protein_abundance_by_marker_location.ipynb
index ed8a6d1..2232f54 100755
--- a/examples/protein_abundance_by_marker_location.ipynb
+++ b/examples/protein_abundance_by_marker_location.ipynb
@@ -425,6 +425,24 @@
     "df1.head(1)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f505f151-7c92-4021-b4b6-da9eb76a4274",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "to_table(df1,f\"{output_dir_path}/01_gfpby_pixels.pqt\") # saved as a parquet file because of its potentially large size "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f2607927-9ed2-4dfb-831a-4f8a1ae73a60",
+   "metadata": {},
+   "source": [
+    "### Aggregation"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 13,
diff --git a/htsimaging/viz/image.py b/htsimaging/viz/image.py
index 67ebb3d..71464b0 100755
--- a/htsimaging/viz/image.py
+++ b/htsimaging/viz/image.py
@@ -47,6 +47,12 @@ def image_background(
             N=50,
             )        
     ax=plt.subplot(111) if ax is None else ax
+    # TODO preprocess
+    # if not rotation is None:
+    #     assert rotation%90 ==0:
+    # img=numpy.rot90(img,3)
+    # img_region=numpy.rot90(img_region,3)
+
     if not img is None:
         ax_img=ax.imshow(
             img,
diff --git a/setup.py b/setup.py
index a6f13ef..277beb9 100755
--- a/setup.py
+++ b/setup.py
@@ -25,6 +25,7 @@
     'scikit-image', # image processing.
     'argh', # for command-line convinience
     'seaborn',
+    'fastparquet',
     ],
 'spt':[
     'pims==0.4.1', 
@@ -66,7 +67,7 @@
     author='rraadd88',
     author_email='rohanadandage@gmail.com',
     license='General Public License v. 3',
-    packages=setuptools.find_packages('.',exclude=['test','tests', 'unit','deps','data','examples']),
+    packages=setuptools.find_packages('.',exclude=['test', 'unit','deps', 'data']),
     classifiers=[
         'Programming Language :: Python',
         'Programming Language :: Python :: 3',
@@ -82,4 +83,4 @@
     # 'console_scripts': ['htsimaging = htsimaging.run:parser.dispatch',],
     # },
     python_requires='>=3.7, <4',
-)
+)
\ No newline at end of file