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Export sim results to json based on Arkheia documentation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,216 @@ | ||
| import os | ||
| import re | ||
| import json | ||
| import numpy as np | ||
| from numpyencoder import NumpyEncoder | ||
| from sphinx.util import docstrings | ||
|
|
||
|
|
||
| PARAMETERS_REGEX = re.compile(".*Parameters.*") | ||
| OTHER_PARAMETER_REGEX = re.compile(".*Other\ [pP]arameters\ *\n-{15}-+") | ||
| PARAMETER_REGEX = re.compile( | ||
| "\s*(?P<name>[^:\s]+)\s*\:\s* (?P<tpe>[^\n]*)\n\s*(?P<doc>[^\n]*)" | ||
| ) | ||
|
|
||
| def save_json(d, filename): | ||
| with open(filename, 'w', encoding='utf-8') as f: | ||
| json.dump(d, f, ensure_ascii=False, indent=4, cls=NumpyEncoder) | ||
|
|
||
| def get_params_from_docstring(cls): | ||
| params = {} | ||
| for cls1 in cls.__mro__: | ||
| params.update(parse_docstring(cls1.__doc__)["params"]) | ||
| return params | ||
|
|
||
| def parse_docstring(docstring): | ||
| """Parse the docstring into its components. | ||
| :returns: a dictionary of form | ||
| { | ||
| "short_description": ..., | ||
| "long_description": ..., | ||
| "params": [{"name": ..., "doc": ...}, ...], | ||
| "returns": ... | ||
| } | ||
| """ | ||
|
|
||
| short_description = long_description = returns = "" | ||
| params = [] | ||
|
|
||
| if docstring: | ||
| docstring = "\n".join(docstrings.prepare_docstring(docstring)) | ||
|
|
||
| lines = docstring.split("\n", 1) | ||
| short_description = lines[0] | ||
|
|
||
| if len(lines) > 1: | ||
| reminder = lines[1].strip() | ||
| # params_returns_desc = None | ||
| match_parameters = PARAMETERS_REGEX.search(reminder) | ||
| if match_parameters: | ||
| long_desc_end = match_parameters.start() | ||
| long_description = reminder[:long_desc_end].rstrip() | ||
| reminder = reminder[long_desc_end:].strip() | ||
|
|
||
| match = OTHER_PARAMETER_REGEX.search(reminder) | ||
|
|
||
| if match: | ||
| end = match.start() | ||
| if not match_parameters: | ||
| long_description = reminder[:end].rstrip() | ||
| reminder = reminder[end:].strip() | ||
|
|
||
| if reminder: | ||
| params = {} | ||
|
|
||
| for name, tpe, doc in PARAMETER_REGEX.findall(reminder): | ||
| params[name] = (tpe, doc) | ||
|
|
||
| if (not match_parameters) and (not match): | ||
| long_description = reminder | ||
|
|
||
| return { | ||
| "short_description": short_description, | ||
| "long_description": long_description, | ||
| "params": params, | ||
| } | ||
|
|
||
| def get_recorders(parameters): | ||
| recorders_docs = [] | ||
| for sh in parameters["sheets"].keys(): | ||
| for rec in parameters["sheets"][sh]["params"]["recorders"].keys(): | ||
| recorder = parameters["sheets"][sh]["params"]["recorders"][rec] | ||
| name = recorder["component"].split(".")[-1] | ||
| module_path = ".".join(recorder["component"].split(".")[:-1]) | ||
| doc_par = get_params_from_docstring( | ||
| getattr(__import__(module_path, globals(), locals(), name), name) | ||
| ) | ||
| p = { | ||
| k: (recorder["params"][k], doc_par[k][0], doc_par[k][1]) | ||
| for k in recorder["params"].keys() | ||
| } | ||
|
|
||
| recorders_docs.append( | ||
| { | ||
| "code": module_path + "." + name, | ||
| "short_description": parse_docstring( | ||
| getattr( | ||
| __import__(module_path, globals(), locals(), name), name | ||
| ).__doc__ | ||
| )["short_description"], | ||
| "long_description": parse_docstring( | ||
| getattr( | ||
| __import__(module_path, globals(), locals(), name), name | ||
| ).__doc__ | ||
| )["long_description"], | ||
| "parameters": p, | ||
| "variables": recorder["variables"], | ||
| "source": sh, | ||
| } | ||
| ) | ||
| return recorders_docs | ||
|
|
||
| def get_experimental_protocols(data_store): | ||
| experimental_protocols_docs = [] | ||
| for ep in data_store.get_experiment_parametrization_list(): | ||
| name = ep[0][8:-2].split(".")[-1] | ||
| module_path = ".".join(ep[0][8:-2].split(".")[:-1]) | ||
| doc_par = get_params_from_docstring( | ||
| getattr(__import__(module_path, globals(), locals(), name), name) | ||
| ) | ||
| params = eval(ep[1]) | ||
|
|
||
| p = { | ||
| k: (params[k], doc_par[k][0], doc_par[k][1]) | ||
| if k in doc_par | ||
| else params[k] | ||
| for k in params.keys() | ||
| } | ||
|
|
||
| experimental_protocols_docs.append( | ||
| { | ||
| "class": module_path + "." + name, | ||
| "short_description": parse_docstring( | ||
| getattr( | ||
| __import__(module_path, globals(), locals(), name), name | ||
| ).__doc__ | ||
| )["short_description"], | ||
| "long_description": parse_docstring( | ||
| getattr( | ||
| __import__(module_path, globals(), locals(), name), name | ||
| ).__doc__ | ||
| )["long_description"], | ||
| "parameters": p, | ||
| } | ||
| ) | ||
| return experimental_protocols_docs | ||
|
|
||
| from mozaik.tools.mozaik_parametrized import MozaikParametrized | ||
|
|
||
| def reduce_dicts(dicts): | ||
| constant = {k : True for k in dicts.keys()} | ||
| for d in dicts(): | ||
| continue | ||
|
|
||
| #changing_parameters = {} | ||
| #unique_stimulus_types = set([MozaikExtendedParameterSet(s).to_dict()["name"] s for s in unique_stimuli]) | ||
| # | ||
| #for s_type in unique_stimulus_types: | ||
| # stim_dicts = [MozaikExtendedParameterSet(s).to_dict() for s in unique_stimuli()] | ||
| # stim_dicts = [d for d in stim_dicts if d["name"] == s_type] | ||
| # changing_parameters["name"] = reduce_dicts(stim_dicts) | ||
| # break | ||
|
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||
| import imageio | ||
|
|
||
| def get_stimuli(data_store, store_stimuli, input_space): | ||
| stim_docs = [] | ||
| if not store_stimuli: | ||
| return stim_docs | ||
| unique_stimuli = [s for s in set(data_store.get_stimuli())] | ||
| stim_dir = "stimuli/" | ||
| os.makedirs(data_store.parameters.root_directory + stim_dir, exist_ok=True) | ||
| for s in unique_stimuli: | ||
| sidd = MozaikParametrized.idd(s) | ||
| params = sidd.get_param_values() | ||
| params = {k: (v, sidd.params()[k].doc) for k, v in params} | ||
|
|
||
| # Only save one trial of each different stimulus | ||
| if params["trial"][0] != 0: | ||
| continue | ||
|
|
||
| raws = data_store.get_sensory_stimulus([s]) | ||
|
|
||
| if raws == [] or raws[0] == None: | ||
| img = np.zeros((50,50)).astype(np.uint8) | ||
| raws = [img,img] | ||
| else: | ||
| raws = raws[0] | ||
|
|
||
| mov_duration = input_space["update_interval"] / 1000.0 if input_space != None else 0.1 | ||
| gif_name = params["name"][0] + str(hash(s)) + ".gif" | ||
| imageio.mimwrite(data_store.parameters.root_directory + stim_dir + gif_name, raws, duration=mov_duration) | ||
|
|
||
| stim_docs.append( | ||
| { | ||
| "code": sidd.name, | ||
| "short_description": parse_docstring( | ||
| getattr( | ||
| __import__( | ||
| sidd.module_path, globals(), locals(), sidd.name | ||
| ), | ||
| sidd.name, | ||
| ).__doc__ | ||
| )["short_description"], | ||
| "long_description": parse_docstring( | ||
| getattr( | ||
| __import__( | ||
| sidd.module_path, globals(), locals(), sidd.name | ||
| ), | ||
| sidd.name, | ||
| ).__doc__ | ||
| )["long_description"], | ||
| "parameters": params, | ||
| "movie": stim_dir + gif_name, | ||
| } | ||
| ) | ||
| return stim_docs |
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