Python 3 compatibility

corticalmapping.egg-info/PKG-INFO

@@ -0,0 +1,20 @@
+Metadata-Version: 2.1
+Name: corticalmapping
+Version: 2.0.0
+Summary: cortical mapping tools
+Home-page: http://stash.corp.alleninstitute.org/users/junz/repos/corticalmapping/
+Author: Jun Zhuang
+Author-email: junz@alleninstitute.org
+License: UNKNOWN
+Description: corticalmapping 
+
+        by Jun Zhuang @ 2014
+
+        contains basic visual stimulation, imaging analysis, plotting, cell visual response properties analysis functionalities.
+        also contains a relatively mature code base of retinotopic mapping (visual stimulation and analysis)
+Platform: any
+Classifier: Programming Language :: Python
+Classifier: Development Status :: 4 - Beta
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Provides-Extra: testing

corticalmapping.egg-info/SOURCES.txt

@@ -0,0 +1,38 @@
+README.md
+setup.py
+corticalmapping/CaimanTools.py
+corticalmapping/CamstimTools.py
+corticalmapping/DatabaseTools.py
+corticalmapping/HighLevel.py
+corticalmapping/MotionCorrection.py
+corticalmapping/NwbTools.py
+corticalmapping/ResponseAnalysis.py
+corticalmapping/RetinotopicMapping.py
+corticalmapping/SingleCellAnalysis.py
+corticalmapping/VasculatureMapMatching.py
+corticalmapping/VisualStim.py
+corticalmapping/__init__.py
+corticalmapping/setup.py
+corticalmapping.egg-info/PKG-INFO
+corticalmapping.egg-info/SOURCES.txt
+corticalmapping.egg-info/dependency_links.txt
+corticalmapping.egg-info/requires.txt
+corticalmapping.egg-info/top_level.txt
+corticalmapping/core/DataAnalysis.py
+corticalmapping/core/FileTools.py
+corticalmapping/core/ImageAnalysis.py
+corticalmapping/core/PlottingTools.py
+corticalmapping/core/TimingAnalysis.py
+corticalmapping/core/__init__.py
+corticalmapping/core/tifffile.py
+corticalmapping/ephys/KilosortWrapper.py
+corticalmapping/ephys/OpenEphysWrapper.py
+corticalmapping/ephys/__init__.py
+corticalmapping/ipython_lizard/__init__.py
+corticalmapping/ipython_lizard/export_notebook_functions.py
+corticalmapping/ipython_lizard/html_widgets.py
+corticalmapping/ipython_lizard/ipython_filedialog.py
+corticalmapping/ipython_lizard/patchplot_ipywidgets.py
+corticalmapping/ipython_lizard/wrapped_retinotopic_mapping.py
+corticalmapping/ipython_lizard/utils/__init__.py
+corticalmapping/ipython_lizard/utils/progress_bar.py

corticalmapping.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

corticalmapping.egg-info/requires.txt

@@ -0,0 +1,8 @@
+numpy
+scipy
+PyDAQmx
+scikit-image
+tifffile
+
+[testing]
+pytest

corticalmapping.egg-info/top_level.txt

@@ -0,0 +1 @@
+corticalmapping

corticalmapping/.gitignore

@@ -0,0 +1,58 @@
+# Created by .ignore support plugin (hsz.mobi)
+### JetBrains template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm
+
+#*.iml
+*.pyc
+
+
+## Directory-based project format:
+.idea/
+.cache/
+
+
+# if you remove the above rule, at least ignore the following:
+
+# User-specific stuff:
+# .idea/workspace.xml
+# .idea/tasks.xml
+# .idea/dictionaries
+
+# Sensitive or high-churn files:
+# .idea/dataSources.ids
+# .idea/dataSources.xml
+# .idea/sqlDataSources.xml
+# .idea/dynamic.xml
+# .idea/uiDesigner.xml
+
+# Gradle:
+# .idea/gradle.xml
+# .idea/libraries
+
+# Mongo Explorer plugin:
+# .idea/mongoSettings.xml
+
+## File-based project format:
+*.ipr
+*.iws
+
+## Plugin-specific files:
+
+# IntelliJ
+/out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+
+
+/corticalmapping/ipython_lizard/res/test_pkls
+.ipynb_checkpoints
+

corticalmapping/DatabaseTools.py

@@ -1717,80 +1717,6 @@ def get_axon_dgcrm_from_clu_f(clu_f, plane_n, axon_n, trace_type):
         return dgcrm
 
 
-def get_axon_morphology(clu_f, nwb_f, plane_n, axon_n):
-
-    axon_morph = {}
-
-    mc_grp = nwb_f['processing/motion_correction/MotionCorrection/{}/corrected'.format(plane_n)]
-    pixel_size = mc_grp['pixel_size'].value
-    # print(pixel_size)
-    pixel_size_mean = np.mean(pixel_size)
-
-    bout_ns = clu_f['axons/{}'.format(axon_n)].value
-    # print(bout_ns)
-    bout_num = len(bout_ns)
-    axon_morph['bouton_num'] = bout_num
-
-    if bout_num == 1:
-        axon_roi = get_roi(nwb_f=nwb_f, plane_n=plane_n, roi_n=bout_ns[0])
-    else:
-        axon_roi = get_axon_roi_from_clu_f(clu_f=clu_f, axon_n=axon_n)
-        axon_roi = ia.WeightedROI(axon_roi.get_weighted_mask(), pixelSize=pixel_size,
-                                  pixelSizeUnit=mc_grp['pixel_size_unit'].value)
-
-    # plt.imshow(axon_roi.get_binary_mask(), interpolation='nearest')
-    # plt.show()
-
-    axon_morph['axon_row_range'] = (np.max(axon_roi.pixels[0]) -
-                                    np.min(axon_roi.pixels[0])) * pixel_size[0] * 1e6
-    axon_morph['axon_col_range'] = (np.max(axon_roi.pixels[1]) -
-                                    np.min(axon_roi.pixels[1])) * pixel_size[1] * 1e6
-
-    axon_morph['axon_area'] = axon_roi.get_pixel_area() * 1e12
-
-    axon_qhull = spatial.ConvexHull(np.array(axon_roi.pixels).transpose())
-    # print(axon_qhull.volume)
-    axon_morph['axon_qhull_area'] = axon_qhull.volume * axon_roi.pixelSizeX * axon_roi.pixelSizeY * 1e12
-
-    bout_rois = []
-    for bout_n in bout_ns:
-        bout_rois.append(get_roi(nwb_f=nwb_f, plane_n=plane_n, roi_n=bout_n))
-
-    bout_areas = [r.get_pixel_area() for r in bout_rois]
-    bout_area_mean = np.mean(bout_areas)
-    axon_morph['bouton_area_mean'] = bout_area_mean * 1e12
-
-    if bout_num == 1:
-        bout_area_std = np.nan
-    else:
-        bout_area_std = np.std(bout_areas)
-    axon_morph['bouton_area_std'] = bout_area_std * 1e12
-
-    bout_coords = np.array([r.get_center() for r in bout_rois]) # [[y0, x0], [y1, x1], ... , [yn, xn]]
-    if bout_num == 1:
-        axon_morph['bouton_row_std'] = np.nan
-        axon_morph['bouton_col_std'] = np.nan
-        axon_morph['bouton_dis_mean'] = np.nan
-        axon_morph['bouton_dis_std'] = np.nan
-        axon_morph['bouton_dis_median'] = np.nan
-        axon_morph['bouton_dis_max'] = np.nan
-    else:
-        axon_morph['bouton_row_std'] = np.std(bout_coords[:, 0]) * pixel_size_mean * 1e6
-        axon_morph['bouton_col_std'] = np.std(bout_coords[:, 1]) * pixel_size_mean * 1e6
-
-        bout_dis = spatial.distance.pdist(bout_coords) * pixel_size_mean
-        axon_morph['bouton_dis_mean'] = np.mean(bout_dis) * 1e6
-        axon_morph['bouton_dis_median'] = np.median(bout_dis) * 1e6
-        axon_morph['bouton_dis_max'] = np.max(bout_dis) * 1e6
-
-        if bout_num == 2:
-            axon_morph['bouton_dis_std'] = np.nan
-        else:
-            axon_morph['bouton_dis_std'] = np.std(bout_dis) * 1e6
-
-    return axon_morph
-
-
 def get_everything_from_axon(nwb_f, clu_f, plane_n, axon_n, params=ANALYSIS_PARAMS, verbose=False):
     """
 
@@ -3819,28 +3745,14 @@ def get_sta(arr, arr_ts, trigger_ts, frame_start, frame_end):
 if __name__ == '__main__':
 
     # ===================================================================================================
-    nwb_f = h5py.File(r"G:\bulk_LGN_database\nwbs\190221_M426525_110_repacked.nwb", 'r')
-    clu_f = h5py.File(r"G:\bulk_LGN_database\intermediate_results\bouton_clustering"
-                      r"\AllStimuli_DistanceThr_1.30\190221_M426525_plane0_axon_grouping.hdf5", 'r')
-    plane_n = 'plane0'
-    axon_n = 'axon_0007'
-    axon_morph = get_axon_morphology(clu_f=clu_f, nwb_f=nwb_f, plane_n=plane_n, axon_n=axon_n)
-
-    keys = axon_morph.keys()
-    keys.sort()
-    for key in keys:
-        print('{}: {}'.format(key, axon_morph[key]))
-    # ===================================================================================================
-
-    # ===================================================================================================
-    # nwb_f = h5py.File(r"G:\bulk_LGN_database\nwbs\190404_M439939_110_repacked.nwb")
-    # uc_inds, _ = get_UC_ts_mask(nwb_f=nwb_f, plane_n='plane0')
-    # plt.plot(uc_inds)
-    # plt.show()
-    #
-    # dgc_spont_inds, _ = get_DGC_spont_ts_mask(nwb_f=nwb_f, plane_n='plane0')
-    # plt.plot(dgc_spont_inds)
-    # plt.show()
+    nwb_f = h5py.File(r"G:\bulk_LGN_database\nwbs\190404_M439939_110_repacked.nwb")
+    uc_inds, _ = get_UC_ts_mask(nwb_f=nwb_f, plane_n='plane0')
+    plt.plot(uc_inds)
+    plt.show()
+
+    dgc_spont_inds, _ = get_DGC_spont_ts_mask(nwb_f=nwb_f, plane_n='plane0')
+    plt.plot(dgc_spont_inds)
+    plt.show()
     # ===================================================================================================
 
     # ===================================================================================================
@@ -3894,6 +3806,4 @@ def get_sta(arr, arr_ts, trigger_ts, frame_start, frame_end):
     # plot_roi_retinotopy(coords_roi=coords_roi, coords_rf=coords_rf, ax_alt=ax_alt, ax_azi=ax_azi,
     #                     cmap='viridis', canvas_shape=(512, 512), edgecolors='#000000', linewidths=0.5)
     # plt.show()
-    # ===================================================================================================
-
-    print('for debug ...')
+    # ===================================================================================================