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R8222/h5parse.py
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h5parse.py
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import os
import h5py
def descend_obj(obj,sep='\t'):
"""
Iterate through groups in a HDF5 file and prints the groups and datasets names and datasets attributes
"""
if type(obj) in [h5py._hl.group.Group,h5py._hl.files.File]:
for key in obj.keys():
print sep,'-',key,':',obj[key]
descend_obj(obj[key],sep=sep+'\t')
elif type(obj)==h5py._hl.dataset.Dataset:
for key in obj.attrs.keys():
print sep+'\t','-',key,':',obj.attrs[key]
def h5dump(path,group='/'):
"""
print HDF5 file metadata
group: you can give a specific group, defaults to the root group
"""
with h5py.File(path,'r') as f:
descend_obj(f[group])
########################################################################
# Parse CellProfiler h5 file
########################################################################
class CPparser(object):
"""
Class to parse a CellProfiler h5 file
"""
SUPPORTED_VERSIONS = ['3.1.8','3.1.5']
def __init__(self, path):
self.path = path
self.obj = h5py.File(path,'r')
self.date = self.obj['/Measurements'].keys()[0]
self.version = self._verify_version()
def _verify_version(self):
"""
Return Cellprofiler version
"""
group = os.path.join('Measurements',
self.date,
'Experiment',
'CellProfiler_Version',
'data')
version = self.obj[group][0]
assert version in self.SUPPORTED_VERSIONS, "Cellprofiler {0} version not supported.".format(version)
return version
def _get_image_group(self):
"""
Return group to images
"""
group = os.path.join('Measurements',
self.date,
'Image',
'PathName_bfimage',
'data')
if self.version == '3.1.5':
temp = group.split('/')
temp[3] = 'PathName_FullStack'
group = os.path.join(*temp)
return group
def get_images_number(self):
"""
Return total number of images
"""
group = self._get_image_group()
return len(self.obj[group])
def get_images_path(self):
"""
Return images
"""
group = self._get_image_group()
return self.obj[group][0]
def h5_obj_print(path):
"""
Print HDF5 file metadata
"""
cp = CPparser(path)
print 'Experiment: {0}'.format(cp.date)
print 'CellProfiler Version: {0}'.format(cp.version)
print 'Number of images: {0}'.format(cp.get_images_number())
print 'Path to images: {0}'.format(cp.get_images_path())
print
if __name__ == "__main__":
h5_obj_print("/home/diego/work/dev/h5_parsing/Batch_data.h5")
h5_obj_print("/home/diego/work/dev/h5_parsing/test/example_csv/Batch_data.h5")
h5_obj_print("/home/diego/work/dev/h5_parsing/test/example_grouping/Batch_data.h5")
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