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Merge pull request #69 from openworm/experimental
Improved Varshney & Witvliet
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| from c302.NeuroMLUtilities import ConnectionInfo | ||
| from c302.NeuroMLUtilities import analyse_connections | ||
| from openpyxl import load_workbook | ||
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| import os | ||
| from c302 import print_ | ||
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| spreadsheet_location = os.path.dirname(os.path.abspath(__file__))+"/data/" | ||
| spreadsheet_name = "NeuronConnect.xlsx" # has old name... | ||
| spreadsheet_name = "NeuronConnectFormatted.xlsx" | ||
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| READER_DESCRIPTION = """Data extracted from %s for neuronal connectivity"""%spreadsheet_name | ||
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| NMJ_ENDPOINT = 'NMJ' | ||
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| def read_data(include_nonconnected_cells=False, neuron_connect=True): | ||
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| if neuron_connect: | ||
| conns = [] | ||
| cells = [] | ||
| filename = "%s%s"%(spreadsheet_location,spreadsheet_name) | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
| print_("Opened the Excel file: " + filename) | ||
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| for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
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| if not post==NMJ_ENDPOINT: | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse' | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in cells: | ||
| cells.append(pre) | ||
| if post not in cells: | ||
| cells.append(post) | ||
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| return cells, conns | ||
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| def read_muscle_data(): | ||
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| conns = [] | ||
| neurons = [] | ||
| muscles = [] | ||
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| filename = "%s%s"%(spreadsheet_location,spreadsheet_name) | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
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| print_("Opened Excel file: "+ filename) | ||
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| for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
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| if post==NMJ_ENDPOINT: | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse' | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in neurons: | ||
| neurons.append(pre) | ||
| if not post in muscles: | ||
| muscles.append(post) | ||
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| return neurons, muscles, conns | ||
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| def main(): | ||
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| cells, neuron_conns = read_data(include_nonconnected_cells=True) | ||
| neurons2muscles, muscles, muscle_conns = read_muscle_data() | ||
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| analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) | ||
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| if __name__ == '__main__': | ||
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| main() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,224 @@ | ||
| from c302.NeuroMLUtilities import ConnectionInfo | ||
| from c302.NeuroMLUtilities import analyse_connections | ||
|
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| from openpyxl import load_workbook | ||
| import os | ||
| from c302 import print_ | ||
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| spreadsheet_location = os.path.dirname(os.path.abspath(__file__))+"/data/" | ||
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| def get_old_muscle_name(name): | ||
| if name.startswith("BWM-VL"): | ||
| return "MVL%s" %name[6:] | ||
| elif name.startswith("BWM-VR"): | ||
| return "MVR%s" %name[6:] | ||
| elif name.startswith("BWM-DL"): | ||
| return "MDL%s" %name[6:] | ||
| elif name.startswith("BWM-DR"): | ||
| return "MDR%s" %name[6:] | ||
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| class WitvlietDataReader1: | ||
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| def read_data(include_nonconnected_cells=False, neuron_connect=False): | ||
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| if neuron_connect: | ||
| conns = [] | ||
| cells = [] | ||
| filename = "%switvliet_2020_7.xlsx"%spreadsheet_location | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
| print_("Opened the Excel file: " + filename) | ||
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| for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in cells: | ||
| cells.append(pre) | ||
| if post not in cells: | ||
| cells.append(post) | ||
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| return cells, conns | ||
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| else: | ||
| conns = [] | ||
| cells = [] | ||
| filename = "%switvliet_2020_7.xlsx"%spreadsheet_location | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
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| print_("Opened Excel file..: " + filename) | ||
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| known_nonconnected_cells = ['CANL', 'CANR', 'VC6'] | ||
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| for row in sheet.iter_rows(min_row=2, values_only=True): | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in cells: | ||
| cells.append(pre) | ||
| if post not in cells: | ||
| cells.append(post) | ||
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| if include_nonconnected_cells: | ||
| for c in known_nonconnected_cells: cells.append(c) | ||
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| return cells, conns | ||
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| def read_muscle_data(): | ||
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| conns = [] | ||
| neurons = [] | ||
| muscles = [] | ||
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| filename = "%switvliet_2020_7.xlsx"%spreadsheet_location | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
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| print_("Opened Excel file: "+ filename) | ||
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| for row in sheet.iter_rows(min_row=2, values_only=True): | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'EJ' in syntype else 'Chemical_Synapse' | ||
| if post.startswith("BWM-"): | ||
| post = get_old_muscle_name(post) | ||
| else: | ||
| continue | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in neurons: | ||
| neurons.append(pre) | ||
| if post not in muscles: | ||
| muscles.append(post) | ||
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| return neurons, muscles, conns | ||
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| def main1(): | ||
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| cells, neuron_conns = WitvlietDataReader1.read_data(include_nonconnected_cells=True) | ||
| neurons2muscles, muscles, muscle_conns = WitvlietDataReader1.read_muscle_data() | ||
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| analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) | ||
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| class WitvlietDataReader2: | ||
| def read_data(include_nonconnected_cells=False, neuron_connect=False): | ||
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| if neuron_connect: | ||
| conns = [] | ||
| cells = [] | ||
| filename = "%switvliet_2020_8.xlsx"%spreadsheet_location | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
| print_("Opened the Excel file: " + filename) | ||
|
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|
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| for row in sheet.iter_rows(min_row=2, values_only=True): # Assuming data starts from the second row | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in cells: | ||
| cells.append(pre) | ||
| if post not in cells: | ||
| cells.append(post) | ||
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| return cells, conns | ||
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| else: | ||
| conns = [] | ||
| cells = [] | ||
| filename = "%switvliet_2020_8.xlsx"%spreadsheet_location | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
|
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| print_("Opened Excel file..: " + filename) | ||
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| known_nonconnected_cells = ['CANL', 'CANR', 'VC6'] | ||
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| for row in sheet.iter_rows(min_row=2, values_only=True): | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' | ||
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in cells: | ||
| cells.append(pre) | ||
| if post not in cells: | ||
| cells.append(post) | ||
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| if include_nonconnected_cells: | ||
| for c in known_nonconnected_cells: cells.append(c) | ||
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| return cells, conns | ||
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| def read_muscle_data(): | ||
|
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| conns = [] | ||
| neurons = [] | ||
| muscles = [] | ||
|
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| filename = "%switvliet_2020_8.xlsx"%spreadsheet_location | ||
| wb = load_workbook(filename) | ||
| sheet = wb.worksheets[0] | ||
|
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| print_("Opened Excel file: "+ filename) | ||
|
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| for row in sheet.iter_rows(min_row=2, values_only=True): | ||
| pre = str(row[0]) | ||
| post = str(row[1]) | ||
| syntype = str(row[2]) | ||
| num = int(row[3]) | ||
| synclass = 'Generic_GJ' if 'electrical' in syntype else 'Chemical_Synapse' | ||
| if post.startswith("BWM-"): | ||
| post = get_old_muscle_name(post) | ||
| else: | ||
| continue | ||
|
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| conns.append(ConnectionInfo(pre, post, num, syntype, synclass)) | ||
| if pre not in neurons: | ||
| neurons.append(pre) | ||
| if post not in muscles: | ||
| muscles.append(post) | ||
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| return neurons, muscles, conns | ||
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| def main2(): | ||
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| cells, neuron_conns = WitvlietDataReader2.read_data(include_nonconnected_cells=True) | ||
| neurons2muscles, muscles, muscle_conns = WitvlietDataReader2.read_muscle_data() | ||
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| analyse_connections(cells, neuron_conns, neurons2muscles, muscles, muscle_conns) | ||
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| if __name__ == '__main__': | ||
| main1() | ||
| main2() |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| __version__ = '0.7.12' | ||
| __version__ = '0.8.0' |
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