diff --git a/.gitignore b/.gitignore index 63cd3785..3e6c6c27 100644 --- a/.gitignore +++ b/.gitignore @@ -90,3 +90,4 @@ arm64 /.ipynb_checkpoints /c302/.ipynb_checkpoints .ipynb_checkpoints +/c302/data/~$*.xlsx diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index d7a49fbc..00000000 --- a/.travis.yml +++ /dev/null @@ -1,62 +0,0 @@ -# Framework for running automated tests on Open Source Brain using Travis-CI. -# See https://github.com/OpenSourceBrain/osb-model-validation for more details - -dist: xenial - -addons: - apt: - packages: - # Requirements for Neuron/OMV/etc - - python-numpy - - python-scipy - - python-tornado - - python-matplotlib - - python-tk - - python-dev - -language: python -python: - - "3.7" - - "3.8" - # - "3.9" # does version of neuron in omv work with py3.9? - - -env: - - OMV_ENGINE=jNeuroML - - OMV_ENGINE=jNeuroML_NEURON - - OMV_ENGINE=jNeuroML_validate - - OMV_ENGINE=NON_OMV_TESTS - - -#before_install: - # To run tests requiring a graphical user interface on Travis CI, use xvfb (X Virtual Framebuffer) to imitate a display. - #- "export DISPLAY=:99.0" - #- "sh -e /etc/init.d/xvfb start" - -install: - # Required to run OMV tests - - pip install git+https://github.com/OpenSourceBrain/osb-model-validation - # NeuroML & main install - - pip install pyNeuroML - - pip install . - # Add openworm bundle owmeta remote - - owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json' - -script: - - omv all -V; export OMV_SUCCESS=$?; echo $OMV_SUCCESS - - echo "Finished all OMV tests" - - omv list -V - - if [[ ${OMV_ENGINE} == "NON_OMV_TESTS" ]]; then echo "Continuing with tests not under OMV..."; else exit $OMV_SUCCESS; fi - - echo "Running non OMV tests..." - - python setup.py install - - - # Testing c302 - - cd c302 - - mkdir examples - - python c302_IClamp.py A - #- omv install NEURON # Need to install NEURON - #- export NEURON_HOME=/home/travis/neuron/nrn/x86_64/ - #- python runAndPlot.py -test - #- python c302_utils.py -nogui - - pip freeze diff --git a/c302/NeuroMLUtilities.py b/c302/NeuroMLUtilities.py index d149c027..3af2715b 100644 --- a/c302/NeuroMLUtilities.py +++ b/c302/NeuroMLUtilities.py @@ -105,7 +105,8 @@ def analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_co print_("Found %i neurons connected to muscles: %s\n"%(len(neurons2muscles), sorted(neurons2muscles))) print_("Found %i muscles connected to neurons: %s\n"%(len(muscles), sorted(muscles))) - print_("Found %i connections between neurons and muscles, e.g. %s\n"%(len(muscle_conns), muscle_conns[0])) + + print_("Found %i connections between neurons and muscles%s\n"%(len(muscle_conns), (', e.g. %s'%muscle_conns[0]) if len(muscle_conns)>0 else '')) nts = {} nts_tot = {} diff --git a/c302/SpreadsheetDataReader.py b/c302/SpreadsheetDataReader.py index 13f0095e..66dc0fda 100644 --- a/c302/SpreadsheetDataReader.py +++ b/c302/SpreadsheetDataReader.py @@ -4,7 +4,7 @@ # A simple script to read the values in CElegansNeuronTables.xls. -# This is on of a number of interchangeable "Readers" which can +# This is one of a number of interchangeable "Readers" which can # be used to get connection data for c302 ############################################################ @@ -20,11 +20,13 @@ from c302 import print_ +READER_DESCRIPTION = """Data extracted from CElegansNeuronTables.xls for neuronal connectivity""" + def read_data(include_nonconnected_cells=False, neuron_connect=False): -# reading the NeuronConnect.xls file if neuron_connect = True +# reading the NeuronConnectFormatted.xls file if neuron_connect = True if neuron_connect: conns = [] cells = [] @@ -53,7 +55,7 @@ def read_data(include_nonconnected_cells=False, neuron_connect=False): filename = "%sCElegansNeuronTables.xls"%spreadsheet_location rb = open_workbook(filename) - print_("Opened Excel file..: " + filename) + print_("Opened Excel file: " + filename) known_nonconnected_cells = ['CANL', 'CANR', 'VC6'] diff --git a/c302/c302_utils.py b/c302/c302_utils.py index f7efa3cf..d81d9fe6 100644 --- a/c302/c302_utils.py +++ b/c302/c302_utils.py @@ -12,8 +12,6 @@ import c302 - - natsort = lambda s: [int(t) if t.isdigit() else t for t in re.split(r'(\d+)', s)] @@ -56,7 +54,8 @@ def plots(a_n, info, cells, dt): a_n_ = a_n[:,::downscale] - plot0 = ax.pcolormesh(a_n_) + cmap = plt.colormaps['jet'] + plot0 = ax.pcolormesh(a_n_, cmap=cmap) ax.set_yticks(np.arange(a_n_.shape[0]) + 0.5, minor=False) ax.set_yticklabels(cells) ax.tick_params(axis='y', labelsize=6) @@ -102,6 +101,7 @@ def generate_traces_plot(config,parameter_set,xvals,yvals,info,labels,save,save_ show_plot_already=False, save_figure_to=(None if not save else save_fig_path%(file_name)), cols_in_legend_box=8, + legend_position = "bottom center", title_above_plot=True) @@ -370,10 +370,12 @@ def _show_conn_matrix(data, t, all_info_pre,all_info_post, type, save_figure_to= plt.title(title) fig.canvas.manager.set_window_title(title) import matplotlib - cm = matplotlib.cm.get_cmap('gist_stern_r') + #cm = matplotlib.cm.get_cmap('gist_stern_r') + cmap = plt.colormaps['gist_stern_r'] + #cmap = plt.colormaps['gist_earth'] - im = plt.imshow(data, cmap=cm, interpolation='nearest',norm=None) + im = plt.imshow(data, cmap=cmap, interpolation='nearest',norm=None) ax = plt.gca(); # Gridlines based on minor ticks @@ -551,12 +553,12 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False): from neuroml.loaders import read_neuroml2_file - configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml','c302_C0_Muscles.net.nml','c302_C0_Pharyngeal.net.nml','c302_C0_Oscillator.net.nml','c302_C0_Full.net.nml'] configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml'] # configs = ['c302_C0_Syns.net.nml'] configs = ['c302_C0_Oscillator.net.nml'] configs = ['c302_C0_Muscles.net.nml'] + configs = ['c302_C0_Syns.net.nml', 'c302_C0_Social.net.nml','c302_C0_Muscles.net.nml','c302_C0_Pharyngeal.net.nml','c302_C0_Oscillator.net.nml','c302_C0_Full.net.nml'] if '-phar' in sys.argv: @@ -566,7 +568,7 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False): nml_doc = read_neuroml2_file('examples/%s'%c) - generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/') + generate_conn_matrix(nml_doc, save_fig_dir='./examples/summary/images') if not '-nogui' in sys.argv: plt.show() diff --git a/examples/summary/images/c302_B_Full_elec_neurons_neurons.png b/examples/summary/images/c302_B_Full_elec_neurons_neurons.png index cad2437d..5394127c 100644 Binary files a/examples/summary/images/c302_B_Full_elec_neurons_neurons.png and b/examples/summary/images/c302_B_Full_elec_neurons_neurons.png differ diff --git a/examples/summary/images/c302_B_Muscles_elec_neurons_neurons.png b/examples/summary/images/c302_B_Muscles_elec_neurons_neurons.png index 7635002b..dde136e7 100644 Binary files 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Parameter set: A; configuration: Full
-Generated on: Tue, 31 Jul 2018 with c302 v0.7.0
Generated on: Wed, 31 Jan 2024 with c302 v0.7.12
\n", - " | SP1 | \n", - "U1 | \n", - "U2 | \n", - "OW | \n", - "NWA | \n", - "|||||
---|---|---|---|---|---|---|---|---|---|---|
Values | \n", - "\n", - " | \n", - " | \n", - " | \n", - " | \n", + " | SpreadsheetData | \n", + "UpdSpreadsheetData | \n", + "UpdSpreadsheetData2 | \n", + "OpenWorm | \n", + "WormNeuroAtlas | \n", "
Num Cells | \n", + "Num Neurons | \n", "302 | \n", "302 | \n", "302 | \n", @@ -153,7 +131,7 @@ "300 | \n", "|||||
Num muscles | \n", + "Num Muscles | \n", "97 | \n", "95 | \n", "95 | \n", @@ -161,7 +139,7 @@ "0 | \n", "|||||
Num conns | \n", + "Num N->N conns | \n", "3363 | \n", "5806 | \n", "5821 | \n", @@ -169,27 +147,45 @@ "1650 | \n", "|||||
#N->Musc | \n", + "Num N with ->M | \n", "127 | \n", "254 | \n", "254 | \n", "159 | \n", "0 | \n", "||||
Num N->M conns | \n", + "564 | \n", + "1118 | \n", + "1118 | \n", + "926 | \n", + "0 | \n", + "|||||
N neurotransmitters | \n", + "Acetylcholine (394) Acetylcholine_Tyramine (29) Dopamine (120) FMRFamide (247) GABA (200) Generic_GJ (1084) Glutamate (962) Octapamine (20) Serotonin (178) Serotonin_Acetylcholine (104) Serotonin_Glutamate (25) | \n",
+ " Acetylcholine (3581) GABA (57) Generic_GJ (2168) | \n",
+ " Acetylcholine (3596) GABA (57) Generic_GJ (2168) | \n",
+ " Acetylcholine (2008) Acetylcholine_GJ (222) Acetylcholine_Tyramine (29) Acetylcholine_Tyramine_GJ (13) Dopamine (98) Dopamine_GJ (13) FMRFamide (170) FMRFamide_GJ (90) FRMFemide (45) FRMFemide_GJ (33) GABA (182) GABA_GJ (76) Generic_GJ (1356) Glutamate (824) Glutamate_GJ (324) Octapamine (19) Octapamine_GJ (4) Serotonin (163) Serotonin_Acetylcholine (91) Serotonin_Acetylcholine_GJ (13) Serotonin_GJ (20) Serotonin_Glutamate (11) Serotonin_Glutamate_GJ (1) | \n",
+ " Generic_GJ (1650) | \n",
+ " |||||
M neurotransmitters | \n", + "**MISSING** (2) Acetylcholine (377) Acetylcholineplus_Tyramine (6) Dopamine (1) FMRFamide (3) FRMFemide (5) GABA (126) Glutamate (35) Serotonin (1) Serotoninplus_Acetylcholine (8) | \n",
+ " Acetylcholine (808) GABA (116) Generic_GJ (194) | \n",
+ " Acetylcholine (808) GABA (116) Generic_GJ (194) | \n",
+ " Acetylcholine (924) Generic_GJ (2) | \n",
+ " \n", + " |