diff --git a/.github/workflows/non_omv.yml b/.github/workflows/non_omv.yml index 918d6f36..af430558 100644 --- a/.github/workflows/non_omv.yml +++ b/.github/workflows/non_omv.yml @@ -14,7 +14,7 @@ jobs: fail-fast: false matrix: runs-on: [ubuntu-latest, macos-12, macos-latest ] - python-version: [ 3.8, 3.9, "3.10" ] + python-version: [ 3.8, 3.9, "3.10", "3.11" ] exclude: - runs-on: macos-latest python-version: "3.8" @@ -43,7 +43,9 @@ jobs: pip list - name: Test OpenWormReader with owmeta + if: ${{ matrix.python-version != '3.11' }} run: | + pip install owmeta>=0.12.3 owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json' python -m c302.OpenWormReader diff --git a/c302/OpenWormReader.py b/c302/OpenWormReader.py index b88f45ca..68a1ad0f 100644 --- a/c302/OpenWormReader.py +++ b/c302/OpenWormReader.py @@ -5,11 +5,15 @@ from c302.NeuroMLUtilities import analyse_connections from c302 import print_, MUSCLE_RE -from owmeta_core.bundle import Bundle -from owmeta_core.context import Context -from owmeta.neuron import Neuron -from owmeta.muscle import BodyWallMuscle -from owmeta.worm import Worm +try: + from owmeta_core.bundle import Bundle + from owmeta_core.context import Context + from owmeta.neuron import Neuron + from owmeta.muscle import BodyWallMuscle + from owmeta.worm import Worm +except: + print("owmeta not installed! Cannot run OpenWormReader") + exit() ############################################################ diff --git a/c302/__init__.py b/c302/__init__.py index 581c08b8..74fcc2fd 100755 --- a/c302/__init__.py +++ b/c302/__init__.py @@ -37,15 +37,22 @@ from lxml import etree import re +import json + import collections -from owmeta_core import __version__ as owc_version -from owmeta_core.bundle import Bundle -from owmeta_core.context import Context -from owmeta import __version__ as owmeta_version -from owmeta.cell import Cell -from owmeta.neuron import Neuron -from owmeta.muscle import Muscle +try: + from owmeta_core import __version__ as owc_version + from owmeta_core.bundle import Bundle + from owmeta_core.context import Context + from owmeta import __version__ as owmeta_version + from owmeta.cell import Cell + from owmeta.neuron import Neuron + from owmeta.muscle import Muscle + owmeta_installed = True +except: + print("owmeta not installed! Proceeding anyway...") + owmeta_installed = False try: from urllib2 import URLError # Python 2 @@ -64,6 +71,8 @@ MUSCLE_RE = re.compile(r'M([VD][LR])(\d+)') +OWMETA_CACHED_DATA_FILE = os.path.dirname(os.path.abspath(__file__))+'/data/owmeta_cache.json' + def print_(msg, print_it=True): # print_it=False when not verbose if print_it: @@ -444,72 +453,88 @@ def elem_in_coll_matches_conn(coll, conn): return True return False +cached_owmeta_data = None def _get_cell_info(bnd, cells): - if bnd is None: - return None + global cached_owmeta_data + #print('------ Getting the cell info for %s'%cells) all_neuron_info = collections.OrderedDict() all_muscle_info = collections.OrderedDict() - ctx = bnd(Context)(ident="http://openworm.org/data").stored - # Go through our list and get the neuron object associated with each name. - # Store these in another list. - fixed_up_names = [] - for name in cells: - match = is_muscle(name) - if match: - name = match.group(1) + str(int(match.group(2))) - fixed_up_names.append(name) - #fixed_up_names.remove('MANAL') - #fixed_up_names.remove('MVULVA') - - for name in fixed_up_names: - cell = next(ctx(Cell).query(name=name).load(), None) - if cell is None: - #print_("No matching cell for %s" % name) - continue - - normalized_name = cell.name() - short = ') %s' % normalized_name - color = '.5 0 0' - if isinstance(cell, Neuron): - neuron_types = cell.type() - if 'sensory' in neuron_types: - short = 'Se%s' % short - color = '1 .2 1' - if 'interneuron' in neuron_types: - short = 'In%s' % short - color = '1 0 .4' - if 'motor' in neuron_types: - short = 'Mo%s' % short - color = '.5 .4 1' - - neurotransmitter = cell.neurotransmitter() - elif isinstance(cell, Muscle): - neuron_types = () - neurotransmitter = () - color = '0 0.6 0' - short = 'Mu%s' % short - else: - # At this point, we should only have Neurons and Muscles because the reader - # filters them out - raise Exception('Got an unexpected cell type') - - short = '(%s' % short - receptor = cell.receptor() - if 'GABA' in neurotransmitter: - short = '- %s' % short - elif len(neurotransmitter) == 0: - short = '? %s' % short - else: - short = '+ %s' % short - info = (cell, neuron_types, receptor, neurotransmitter, short, color) + if bnd is None: + if cached_owmeta_data == None: + print_('Loading owmeta cached data from: %s'%OWMETA_CACHED_DATA_FILE) + with open(OWMETA_CACHED_DATA_FILE) as f: + cached_owmeta_data = json.load(f) + + for cell in cells: + if is_muscle(cell): + all_muscle_info[cell] = cached_owmeta_data['muscle_info'][cell] + else: + all_neuron_info[cell] = cached_owmeta_data['neuron_info'][cell] + + else: + ctx = bnd(Context)(ident="http://openworm.org/data").stored + # Go through our list and get the neuron object associated with each name. + # Store these in another list. + fixed_up_names = [] + for name in cells: + match = is_muscle(name) + if match: + name = match.group(1) + str(int(match.group(2))) + fixed_up_names.append(name) + #fixed_up_names.remove('MANAL') + #fixed_up_names.remove('MVULVA') + + for name in fixed_up_names: + cell = next(ctx(Cell).query(name=name).load(), None) + if cell is None: + #print_("No matching cell for %s" % name) + continue + + normalized_name = cell.name() + short = ') %s' % normalized_name + color = '.5 0 0' + if isinstance(cell, Neuron): + neuron_types = cell.type() + if 'sensory' in neuron_types: + short = 'Se%s' % short + color = '1 .2 1' + if 'interneuron' in neuron_types: + short = 'In%s' % short + color = '1 0 .4' + if 'motor' in neuron_types: + short = 'Mo%s' % short + color = '.5 .4 1' + + neurotransmitter = cell.neurotransmitter() + elif isinstance(cell, Muscle): + neuron_types = () + neurotransmitter = () + color = '0 0.6 0' + short = 'Mu%s' % short + else: + # At this point, we should only have Neurons and Muscles because the reader + # filters them out + raise Exception('Got an unexpected cell type') + + short = '(%s' % short + receptor = cell.receptor() + if 'GABA' in neurotransmitter: + short = '- %s' % short + elif len(neurotransmitter) == 0: + short = '? %s' % short + else: + short = '+ %s' % short + + info = (cell, neuron_types, receptor, neurotransmitter, short, color) - if isinstance(cell, Muscle): - all_muscle_info[cell.name()] = info - elif isinstance(cell, Neuron): - all_neuron_info[cell.name()] = info + if isinstance(cell, Muscle): + all_muscle_info[cell.name()] = info + elif isinstance(cell, Neuron): + all_neuron_info[cell.name()] = info + #print('==== Returning %s; %s'%(all_neuron_info, all_muscle_info)) return all_neuron_info, all_muscle_info @@ -618,8 +643,8 @@ def generate(net_id, info = "\n\nParameters and setting used to generate this network:\n\n"+\ " Data reader: %s\n" % data_reader+\ " c302 version: %s\n" % __version__+\ - " owmeta version: %s\n" % owmeta_version+\ - " owmeta_core version: %s\n" % owc_version+\ + " owmeta version: %s\n" % ('- not installed -' if not owmeta_installed else owmeta_version) +\ + " owmeta_core version: %s\n" % ('- not installed -' if not owmeta_installed else owc_version) +\ " Cells: %s\n" % (cells if cells is not None else "All cells")+\ " Cell stimulated: %s\n" % (cells_to_stimulate if cells_to_stimulate is not None else "All neurons")+\ " Connection: %s\n" % (conns_to_include if conns_to_include is not None else "All connections") + \ @@ -727,13 +752,14 @@ def generate(net_id, cells_vs_name = c302.backers.get_adopted_cell_names() count = 0 + try: with Bundle('openworm/owmeta-data', version=6) as bnd: all_neuron_info, all_muscle_info = _get_cell_info(bnd, set(cell_names)) except Exception as e: print_('Unable to open "openworm/owmeta-data" bundle: %s' % e) - all_neuron_info = None - all_muscle_info = None + all_neuron_info, all_muscle_info = _get_cell_info(None, set(cell_names)) + for cell in cell_names: if cells is None or cell in cells: @@ -1489,4 +1515,46 @@ def main(): if __name__ == '__main__': - main() + + import sys + + if '-cache' in sys.argv: + print('Starting c302...') + from c302.ConnectomeReader import PREFERRED_MUSCLE_NAMES + from c302.ConnectomeReader import PREFERRED_NEURON_NAMES + + all_info = {'neuron_info':{}, 'muscle_info':{}} + + + from owmeta_core.bundle import Bundle + + from owmeta_core import __version__ as owc_version + from owmeta import __version__ as owmeta_version + + ver_info = 'owmeta v%s (owmeta core v%s)'%(owmeta_version,owc_version) + all_info['comment'] = 'Information exported from '+ver_info + + with Bundle('openworm/owmeta-data', version=6) as bnd: + + for n in PREFERRED_NEURON_NAMES: + + ani, _all_muscle_info = _get_cell_info(bnd, [n]) + + print(' > %s; %s'%(ani[n], _all_muscle_info)) + all_info['neuron_info'][n] = (str(ani[n][0]),sorted(list(ani[n][1])),sorted(list(ani[n][2])),sorted(list(ani[n][3])),ani[n][4],ani[n][5]) + + for n in PREFERRED_MUSCLE_NAMES: + + _all_neuron_info, ami = _get_cell_info(bnd, [n]) + + if not n == 'MVULVA' and not n == 'MANAL': + ow_name = n[1:] if n[3]!='0' else '%s%s'%(n[1:3],n[-1]) + print(' > %s (%s): %s; %s'%(n, ow_name, _all_neuron_info, ami)) + + all_info['muscle_info'][n] = (str(ami[ow_name][0]),sorted(list(ami[ow_name][1])),sorted(list(ami[ow_name][2])),sorted(list(ami[ow_name][3])),ami[ow_name][4],ami[ow_name][5]) + + with open(OWMETA_CACHED_DATA_FILE, 'w') as fp: + json.dump(all_info, fp, sort_keys=True, indent=4) + + else: + main() diff --git a/c302/backers.py b/c302/backers.py index 377b0c89..84ff8938 100644 --- a/c302/backers.py +++ b/c302/backers.py @@ -1,7 +1,7 @@ ''' This method reads a generated list of cells vs. names as assigned by OpenWorm backers - This information will eventually be moved to owmeta + This information will eventually be moved to owmeta/elsewhere... ''' import os diff --git a/c302/c302_utils.py b/c302/c302_utils.py index e1e7e0fd..0ce89621 100644 --- a/c302/c302_utils.py +++ b/c302/c302_utils.py @@ -8,7 +8,6 @@ import numpy as np from pyneuroml import pynml from pyneuroml import plot as pyneuroml_plot -from owmeta_core.bundle import Bundle import c302 @@ -18,7 +17,6 @@ def plots(a_n, info, cells, dt): - c302.print_('Generating plots for: %s'%info) heightened = False @@ -455,12 +453,23 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=defa all_cells = sorted(all_cells) + all_neurons = [] + all_muscles = [] + for c in all_cells: + if c302.is_muscle(c): + all_muscles.append(c) + else: + all_neurons.append(c) + try: + from owmeta_core.bundle import Bundle with Bundle('openworm/owmeta-data', version=6) as bnd: all_neuron_info, all_muscle_info = c302._get_cell_info(bnd, all_cells) except Exception as e: - c302.print_('Unable to connect to owmeta bundle: %s' % e) traceback.print_exc() + c302.print_('Unable to connect to the owmeta bundle: %s\n Proceeding anyway...' % e) + all_neuron_info, all_muscle_info = c302._get_cell_info(None, all_cells) + ''' if order_by_type: @@ -478,13 +487,6 @@ def generate_conn_matrix(nml_doc, save_fig_dir=None, verbose=False, figsize=defa print('Swapping %s with %s'%(all_neuron_info,ordered_all_neuron_info)) all_neuron_info = ordered_all_neuron_info''' - all_neurons = [] - all_muscles = [] - for c in all_cells: - if c302.is_muscle(c): - all_muscles.append(c) - else: - all_neurons.append(c) data_exc_n = np.zeros((len(all_neurons),len(all_neurons))) diff --git a/c302/data/owmeta_cache.json b/c302/data/owmeta_cache.json new file mode 100644 index 00000000..ebc9abc1 --- /dev/null +++ b/c302/data/owmeta_cache.json @@ -0,0 +1,6038 @@ +{ + "comment": "Information exported from owmeta v0.12.3 (owmeta core v0.13.5)", + "muscle_info": { + "MDL01": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL1", + "0 0.6 0" + ], + "MDL02": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL2", + "0 0.6 0" + ], + "MDL03": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL3", + "0 0.6 0" + ], + "MDL04": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL4", + "0 0.6 0" + ], + "MDL05": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL5", + "0 0.6 0" + ], + "MDL06": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL6", + "0 0.6 0" + ], + "MDL07": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL7", + "0 0.6 0" + ], + "MDL08": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL8", + "0 0.6 0" + ], + "MDL09": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL9", + "0 0.6 0" + ], + "MDL10": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL10", + "0 0.6 0" + ], + "MDL11": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL11", + "0 0.6 0" + ], + "MDL12": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL12", + "0 0.6 0" + ], + "MDL13": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL13", + "0 0.6 0" + ], + "MDL14": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL14", + "0 0.6 0" + ], + "MDL15": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL15", + "0 0.6 0" + ], + "MDL16": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL16", + "0 0.6 0" + ], + "MDL17": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL17", + "0 0.6 0" + ], + "MDL18": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL18", + "0 0.6 0" + ], + "MDL19": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL19", + "0 0.6 0" + ], + "MDL20": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL20", + "0 0.6 0" + ], + "MDL21": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL21", + "0 0.6 0" + ], + "MDL22": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL22", + "0 0.6 0" + ], + "MDL23": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL23", + "0 0.6 0" + ], + "MDL24": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DL24", + "0 0.6 0" + ], + "MDR01": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR1", + "0 0.6 0" + ], + "MDR02": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR2", + "0 0.6 0" + ], + "MDR03": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR3", + "0 0.6 0" + ], + "MDR04": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR4", + "0 0.6 0" + ], + "MDR05": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR5", + "0 0.6 0" + ], + "MDR06": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR6", + "0 0.6 0" + ], + "MDR07": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR7", + "0 0.6 0" + ], + "MDR08": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR8", + "0 0.6 0" + ], + "MDR09": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR9", + "0 0.6 0" + ], + "MDR10": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR10", + "0 0.6 0" + ], + "MDR11": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR11", + "0 0.6 0" + ], + "MDR12": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR12", + "0 0.6 0" + ], + "MDR13": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR13", + "0 0.6 0" + ], + "MDR14": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR14", + "0 0.6 0" + ], + "MDR15": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR15", + "0 0.6 0" + ], + "MDR16": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR16", + "0 0.6 0" + ], + "MDR17": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR17", + "0 0.6 0" + ], + "MDR18": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR18", + "0 0.6 0" + ], + "MDR19": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR19", + "0 0.6 0" + ], + "MDR20": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR20", + "0 0.6 0" + ], + "MDR21": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR21", + "0 0.6 0" + ], + "MDR22": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR22", + "0 0.6 0" + ], + "MDR23": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR23", + "0 0.6 0" + ], + "MDR24": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) DR24", + "0 0.6 0" + ], + "MVL01": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL1", + "0 0.6 0" + ], + "MVL02": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL2", + "0 0.6 0" + ], + "MVL03": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL3", + "0 0.6 0" + ], + "MVL04": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL4", + "0 0.6 0" + ], + "MVL05": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL5", + "0 0.6 0" + ], + "MVL06": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL6", + "0 0.6 0" + ], + "MVL07": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL7", + "0 0.6 0" + ], + "MVL08": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL8", + "0 0.6 0" + ], + "MVL09": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL9", + "0 0.6 0" + ], + "MVL10": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL10", + "0 0.6 0" + ], + "MVL11": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL11", + "0 0.6 0" + ], + "MVL12": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL12", + "0 0.6 0" + ], + "MVL13": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL13", + "0 0.6 0" + ], + "MVL14": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL14", + "0 0.6 0" + ], + "MVL15": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL15", + "0 0.6 0" + ], + "MVL16": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL16", + "0 0.6 0" + ], + "MVL17": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL17", + "0 0.6 0" + ], + "MVL18": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL18", + "0 0.6 0" + ], + "MVL19": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL19", + "0 0.6 0" + ], + "MVL20": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL20", + "0 0.6 0" + ], + "MVL21": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL21", + "0 0.6 0" + ], + "MVL22": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL22", + "0 0.6 0" + ], + "MVL23": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VL23", + "0 0.6 0" + ], + "MVR01": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VR1", + "0 0.6 0" + ], + "MVR02": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VR2", + "0 0.6 0" + ], + "MVR03": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VR3", + "0 0.6 0" + ], + "MVR04": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VR4", + "0 0.6 0" + ], + "MVR05": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VR5", + "0 0.6 0" + ], + "MVR06": [ + "BodyWallMuscle()", + [], + [], + [], + "? (Mu) VR6", + "0 0.6 0" + ], + "MVR07": [ + "BodyWallMuscle()", + [], + [], + [], + "? 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