Merge branch 'dev' into feature/clustering

scripts/create_multi_session_df.py

@@ -7,20 +7,21 @@
 import visual_behavior.ophys.io.create_multi_session_df as io
 
 
-
 if __name__ == '__main__':
     import sys
     project_code = sys.argv[1][1:-1]
     session_number = int(sys.argv[2][:-1])
     print(project_code, session_number)
 
-    # df_name = 'trials_response_df'
-    # conditions = ['cell_specimen_id', 'go', 'hit', 'image_name']
-    # conditions = ['cell_specimen_id', 'change', 'image_name', 'epoch']
+    df_name = 'trials_licks_df'
+    conditions = ['trials_id', 'go', 'hit']
+
+    df = io.get_multi_session_df(project_code, session_number, df_name, conditions, use_events=False, use_extended_stimulus_presentations=True)
+    print('done')
 
-    df_name = 'trials_pupil_area_df'
-    conditions = ['cell_specimen_id', 'go', 'hit', 'image_name']
-    # conditions = ['ophys_experiment_id', 'change', 'image_name', 'licked', 'hit_bout']
+    df_name = 'omission_licks_df'
+    conditions = ['stimulus_presentations_id']
 
-    df = io.get_multi_session_df(project_code, session_number, df_name, conditions, use_events=True, use_extended_stimulus_presentations=True)
-    print('done')
+    df = io.get_multi_session_df(project_code, session_number, df_name, conditions, use_events=False,
+                                 use_extended_stimulus_presentations=True)
+    print('done')

scripts/generate_timeseries_plots.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+
+import os
+import numpy as np
+import pandas as pd
+import visual_behavior.data_access.loading as loading
+from visual_behavior.visualization.ophys import timeseries_figures as tf
+
+
+if __name__ == '__main__':
+    import sys
+    experiment_id = sys.argv[1]
+
+    dataset = loading.get_ophys_dataset(experiment_id)
+    experiments_table = loading.get_filtered_ophys_experiment_table()
+    ophys_session_id = experiments_table.loc[int(experiment_id)].ophys_session_id
+
+    xlim_seconds = [400, 450]
+    tf.plot_behavior_and_pop_avg(dataset, xlim_seconds, save_figure=True)
+    xlim_seconds = [500, 600]
+    tf.plot_behavior_and_cell_traces_pop_avg(dataset, xlim_seconds, save_figure=True)
+    tf.plot_behavior_and_pop_avg_mesoscope(ophys_session_id, xlim_seconds=xlim_seconds, save_figure=True)
+
+    xlim_seconds = [3400, 3450]
+    tf.plot_behavior_and_pop_avg(dataset, xlim_seconds, save_figure=True)
+    xlim_seconds = [3500, 3600]
+    tf.plot_behavior_and_cell_traces_pop_avg(dataset, xlim_seconds, save_figure=True)
+    tf.plot_behavior_and_pop_avg_mesoscope(ophys_session_id, xlim_seconds=xlim_seconds, save_figure=True)
+
+    xlim_seconds = None
+    tf.plot_behavior_and_pop_avg(dataset, xlim_seconds, save_figure=True)
+    tf.plot_behavior_and_cell_traces_pop_avg(dataset, xlim_seconds, save_figure=True)
+    tf.plot_behavior_and_pop_avg_mesoscope(ophys_session_id, xlim_seconds=None, save_figure=True)

scripts/run_create_multi_session_df.py

@@ -4,7 +4,7 @@
 if platform.system() == 'Linux':
     # sys.path.append('/allen/programs/braintv/workgroups/nc-ophys/Doug/pbstools')
     sys.path.append('/allen/programs/braintv/workgroups/nc-ophys/nick.ponvert/src/pbstools')
-from pbstools import PythonJob # flake8: noqa: E999
+from pbstools import PythonJob  # flake8: noqa: E999
 
 
 import visual_behavior.data_access.loading as loading
@@ -30,6 +30,6 @@
             python_executable='/home/marinag/anaconda2/envs/visual_behavior_sdk/bin/python',
             python_args=[project_code, session_number],
             conda_env=None,
-            jobname='multi_session_df_'+project_code+'_'+str(session_number),
+            jobname='multi_session_df_' + project_code + '_' + str(session_number),
             **job_settings
         ).run(dryrun=False)

scripts/run_generate_timeseries_plots.py

@@ -0,0 +1,33 @@
+import os
+import sys
+import platform
+if platform.system() == 'Linux':
+    # sys.path.append('/allen/programs/braintv/workgroups/nc-ophys/Doug/pbstools')
+    sys.path.append('/allen/programs/braintv/workgroups/nc-ophys/nick.ponvert/src/pbstools')
+from pbstools import PythonJob # flake8: noqa: E999
+
+
+import visual_behavior.data_access.loading as loading
+experiments_table = loading.get_filtered_ophys_experiment_table()
+experiment_ids = experiments_table.index.values
+
+python_file = r"/home/marinag/visual_behavior_analysis/scripts/generate_timeseries_plots.py"
+
+jobdir = '/allen/programs/braintv/workgroups/nc-ophys/Marina/ClusterJobs/JobRecords2'
+
+job_settings = {'queue': 'braintv',
+                'mem': '40g',
+                'walltime': '10:00:00',
+                'ppn': 1,
+                'jobdir': jobdir,
+                }
+
+for experiment_id in experiment_ids:
+    PythonJob(
+        python_file,
+        python_executable='/home/marinag/anaconda2/envs/visual_behavior_sdk/bin/python',
+        python_args=experiment_id,
+        conda_env=None,
+        jobname='process_{}'.format(experiment_id),
+        **job_settings
+    ).run(dryrun=False)

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = visual-behavior
-version = 0.10.0
+version = 0.12.0
 description = "analysis package for visual behavior"
 authors = ["Marina Garrett", "Doug Ollerenshaw"]
 author_email="[email protected], [email protected]",
@@ -9,15 +9,15 @@ url = "https://github.com/AllenInstitute/visual_behavior_analysis"
 [options]
 packages=find:
 install_requires =
-    allensdk==2.8.0
-    scikit-learn==0.20.4
-    python-dateutil>=2.6.1
-    zipfile36
-    pymongo
-    pyyaml
-    opencv-python
-    dash
-    plotly
+	allensdk==2.10.2
+	scikit-learn==0.20.4
+	python-dateutil>=2.6.1
+	zipfile36
+	pymongo
+	pyyaml
+	opencv-python
+	dash
+	plotly
 
 [options.extras_require]
 DEV =
@@ -29,7 +29,7 @@ DEV =
     coverage
 
 [bumpversion]
-current_version = 0.8.1.dev0
+current_version = 0.13.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<release>[a-z]+)(?P<n>\d+))?

tests/data_access/test_loading.py

@@ -1,6 +1,8 @@
 import os
 import pytest
 
+def test_basic_import():
+    from visual_behavior.data_access import loading
 
 @pytest.mark.onprem
 def test_get_filtered_ophys_session_table():

tests/test_utilities.py

@@ -21,7 +21,7 @@ def test_find_nearest_index():
 
 @pytest.mark.skipif(not os.path.exists('//allen/programs/braintv'), reason="no access to network path, skipping test on network PKL files")
 def test_movie_load():
-    movie_path = "/allen/programs/braintv/workgroups/nc-ophys/visual_behavior/test_fixtures/853773937_video-0.avi"
+    movie_path = "//allen/programs/braintv/workgroups/nc-ophys/visual_behavior/test_fixtures/853773937_video-0.avi"
     movie = Movie(movie_path)
 
     # get frame by timestamp

visual_behavior/__init__.py

@@ -1 +1,2 @@
-__version__ = "0.10.0"
+
+__version__ = "0.13.0"