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Merge pull request #184 from NeuralEnsemble/feat/document-writers
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docs(writers): document classes and methods
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@sanjayankur31
sanjayankur31 authored Dec 5, 2023
2 parents 5b66349 + 74c442f commit a7e13f8
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Showing 3 changed files with 127 additions and 33 deletions.
9 changes: 8 additions & 1 deletion neuroml/nml/helper_methods.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2931,7 +2931,14 @@ def __str__(self):
source='''\
def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file. """
"""Export to HDF5 file.
:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group
"""
#print("Exporting %s: "+str(self.id)+" as HDF5")
%s
'''
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60 changes: 51 additions & 9 deletions neuroml/nml/nml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@
# -*- coding: utf-8 -*-

#
# Generated Wed Sep 20 19:12:47 2023 by generateDS.py version 2.43.1.
# Python 3.10.6 (main, Nov 14 2022, 16:10:14) [GCC 11.3.0]
# Generated Tue Dec 5 10:44:41 2023 by generateDS.py version 2.43.3.
# Python 3.11.6 (main, Oct 3 2023, 00:00:00) [GCC 13.2.1 20230918 (Red Hat 13.2.1-3)]
#
# Command line options:
# ('-o', 'nml.py')
Expand All @@ -16,7 +16,7 @@
# NeuroML_v2.3.xsd
#
# Command line:
# /usr/local/bin/generateDS -o "nml.py" --use-getter-setter="none" --user-methods="helper_methods.py" --export="write validate" --custom-imports-template="gds_imports-template.py" NeuroML_v2.3.xsd
# /home/asinha/.local/share/virtualenvs/neuroml-311-dev/bin/generateDS -o "nml.py" --use-getter-setter="none" --user-methods="helper_methods.py" --export="write validate" --custom-imports-template="gds_imports-template.py" NeuroML_v2.3.xsd
#
# Current working directory (os.getcwd()):
# nml
Expand Down Expand Up @@ -7370,7 +7370,14 @@ def _buildChildren(
super(InputList, self)._buildChildren(child_, node, nodeName_, True)

def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file."""
"""Export to HDF5 file.

:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group

"""
# print("Exporting InputList: "+str(self.id)+" as HDF5")

ilGroup = h5file.create_group(h5Group, "inputList_" + self.id)
Expand Down Expand Up @@ -10840,7 +10847,14 @@ def _buildChildren(
super(Population, self)._buildChildren(child_, node, nodeName_, True)

def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file."""
"""Export to HDF5 file.

:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group

"""
# print("Exporting Population: "+str(self.id)+" as HDF5")

popGroup = h5file.create_group(h5Group, "population_" + self.id)
Expand Down Expand Up @@ -12504,7 +12518,14 @@ def __str__(self):
)

def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file."""
"""Export to HDF5 file.

:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group

"""
# print("Exporting Network: "+str(self.id)+" as HDF5")

netGroup = h5file.create_group(h5Group, "network")
Expand Down Expand Up @@ -44993,7 +45014,14 @@ def _buildChildren(
super(ContinuousProjection, self)._buildChildren(child_, node, nodeName_, True)

def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file."""
"""Export to HDF5 file.

:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group

"""
# print("Exporting ContinuousProjection: "+str(self.id)+" as HDF5")

projGroup = h5file.create_group(h5Group, "projection_" + self.id)
Expand Down Expand Up @@ -45401,7 +45429,14 @@ def _buildChildren(
super(ElectricalProjection, self)._buildChildren(child_, node, nodeName_, True)

def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file."""
"""Export to HDF5 file.

:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group

"""
# print("Exporting ElectricalProjection: "+str(self.id)+" as HDF5")

projGroup = h5file.create_group(h5Group, "projection_" + self.id)
Expand Down Expand Up @@ -46678,7 +46713,14 @@ def _buildChildren(
super(Projection, self)._buildChildren(child_, node, nodeName_, True)

def exportHdf5(self, h5file, h5Group):
"""Export to HDF5 file."""
"""Export to HDF5 file.

:param h5file: HDF5 file handler
:type h5file: file object
:param h5Group: the tables Group object to write
:type h5Group: tables.Group

"""
# print("Exporting Projection: "+str(self.id)+" as HDF5")

projGroup = h5file.create_group(h5Group, "projection_" + self.id)
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91 changes: 68 additions & 23 deletions neuroml/writers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,25 @@
from six import string_types


"""Classes to write NeuroML to various formats."""


class NeuroMLWriter(object):
"""Writes from NeuroMLDocument to nml file.
In future can implement from other types via chain of responsibility pattern.
"""
@classmethod
def write(cls, nmldoc, file, close=True):
"""
Writes from NeuroMLDocument to nml file
in future can implement from other types
via chain of responsibility pattern.
"""Write a NeuroMLDocument to file.
:param nmldoc: NeuroML document object to write
:type nmldoc: neuroml.NeuroMLDocument
:param file: file name to write to
:type file: str
:param close: toggle whether file should be closed
:type close: bool
:raises AttributeError: if export fails
"""

if isinstance(file, string_types):
Expand Down Expand Up @@ -36,8 +48,21 @@ def write(cls, nmldoc, file, close=True):


class NeuroMLHdf5Writer(object):
"""Exports NeuroML documents to HDF5 format."""
@classmethod
def write(cls, nml_doc, h5_file_name, embed_xml=True, compress=True):
"""Write a NeuroMLDocument to HDF5 file
:param nmldoc: NeuroML document object to write
:type nmldoc: neuroml.NeuroMLDocument
:param h5_file_name: file name to write to
:type h5_file_name: str
:param embed_xml: toggle whether XML serialization should be embedded
:type embed_xml: bool
:param compress: toggle compression
:type compress: bool
"""

import tables

FILTERS = (
Expand Down Expand Up @@ -67,17 +92,13 @@ def write(cls, nml_doc, h5_file_name, embed_xml=True, compress=True):

try:
import StringIO

sf = StringIO.StringIO()
except:
except ImportError:
import io

sf = io.StringIO()

NeuroMLWriter.write(nml_doc, sf, close=False)

nml2 = sf.getvalue()

rootGroup._f_setattr("neuroml_top_level", nml2)

# Put back into previous form...
Expand All @@ -89,20 +110,20 @@ def write(cls, nml_doc, h5_file_name, embed_xml=True, compress=True):
"""
@classmethod
def write_xml_and_hdf5(cls,nml_doc0,xml_file_name,h5_file_name):
nml_doc_hdf5 = neuroml.NeuroMLDocument(nml_doc0.id)
for n in nml_doc0.networks:
nml_doc_hdf5.networks.append(n)
nml_doc0.networks = []
nml_doc0.includes.append(neuroml.IncludeType(h5_file_name))
nml_doc0.includes.append(neuroml.IncludeType(h5_file_name))
NeuroMLWriter.write(nml_doc0,xml_file_name)
NeuroMLHdf5Writer.write(nml_doc_hdf5,h5_file_name,embed_xml=False)
# Put back into previous form...
for n in nml_doc_hdf5.networks:
nml_doc0.networks.append(n)
Expand All @@ -113,11 +134,22 @@ def write_xml_and_hdf5(cls,nml_doc0,xml_file_name,h5_file_name):

class ArrayMorphWriter(object):
"""
Write morphology to ArrayMorph format.
For now just testing a simple method which can write a morphology, not a NeuroMLDocument.
"""

@classmethod
def __write_single_cell(cls, array_morph, fileh, cell_id=None):
"""Write a array morphology to a file handler.
:param array_morph: a array morph object containing a morphology
:type array_morph: neuroml.arraymorph.ArrayMorphology
:param fileh: file handler of file to write to
:type fileh: file object
:param cell_id: id of cell
:type cell_id: str
"""
vertices = array_morph.vertices
connectivity = array_morph.connectivity
physical_mask = array_morph.physical_mask
Expand All @@ -128,12 +160,12 @@ def __write_single_cell(cls, array_morph, fileh, cell_id=None):
# Create the groups:
# can use morphology name in future?

if array_morph.id == None:
if array_morph.id is None:
morphology_name = "Morphology"
else:
morphology_name = array_morph.id

if cell_id == None:
if cell_id is None:
morphology_group = fileh.create_group(root, morphology_name)
hierarchy_prefix = "/" + morphology_name
else:
Expand All @@ -151,26 +183,39 @@ def __write_single_cell(cls, array_morph, fileh, cell_id=None):

@classmethod
def __write_neuroml_document(cls, document, fileh):
document_id = document.id
"""Write a NeuroMLDocument containing morphology to a file handler
:param document: a NeuroML document object containing a morphology
:type document: neuroml.NeuroMLDocument
:param fileh: file handler of file to write to
:type fileh: file object
"""
for default_id, cell in enumerate(document.cells):
morphology = cell.morphology

if morphology.id == None:
if morphology.id is None:
morphology.id = "Morphology" + str(default_id)
if cell.id == None:
if cell.id is None:
cell.id = "Cell" + str(default_id)

cls.__write_single_cell(morphology, fileh, cell_id=cell.id)

for default_id, morphology in enumerate(document.morphology):
if morphology.id == None:
if morphology.id is None:
morphology.id = "Morphology" + str(default_id)

cls.__write_single_cell(morphology, fileh, cell_id=cell.id)

@classmethod
def write(cls, data, filepath):
"""Write morphology to file in ArrayMorph format.
:param data: data to write
:type data: neuroml.arraymorph.ArrayMorphology or neuroml.NeuroMLDocument
:param filepath: path of file to write to
:type filepath: str
"""
import tables

fileh = tables.open_file(filepath, mode="w")
Expand Down

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