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attempt to make file paths also work in windows 

fixes #1
This commit is contained in:
Guillaume Raffy 2020-03-24 19:41:06 +01:00
parent 7103ea2a97
commit 693b8de376
2 changed files with 22 additions and 12 deletions
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24
src/lipase/catalog.py
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@ -25,19 +25,26 @@ class DacMetadata(object):
class Sequence(object): class Sequence(object):
def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path): def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path):
"""
:param Catalog catalog:
:param str sequence_id: eg 'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'
:param str micro_manager_metadata_file_path: eg '/Users/graffy/ownCloud/ipr/lipase/raw-images/res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/metadata.txt'
"""
self.catalog = catalog self.catalog = catalog
self.sequence_id = sequence_id self.sequence_id = sequence_id
self.micro_manager_metadata_file_path = micro_manager_metadata_file_path self.micro_manager_metadata_file_path = micro_manager_metadata_file_path
print(micro_manager_metadata_file_path) print(micro_manager_metadata_file_path)
print('reading micro manager metatdata from %s' % micro_manager_metadata_file_path) print('reading micro manager metatdata from %s' % micro_manager_metadata_file_path)
# note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments) # note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments)
with open(micro_manager_metadata_file_path, "r") as mmm_file: with open(os.path.realpath(micro_manager_metadata_file_path), "r") as mmm_file:
self.mmm = json.load(mmm_file, encoding='latin-1') # note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments) self.mmm = json.load(mmm_file, encoding='latin-1') # note : the micromanager metadata files are encoded in latin-1, not utf8 (see accents in comments)
micro_manager_metadata_file_parent_path = '/'.join(micro_manager_metadata_file_path.split('/')[0:-2]) (pos_dir_path, file_name) = os.path.split(micro_manager_metadata_file_path) # pylint: disable=unused-variable
(micro_manager_metadata_file_parent_path, pos_dir_name) = os.path.split(pos_dir_path) # pylint: disable=unused-variable
assert pos_dir_name[0:3] == 'Pos', 'unexpected value : %s is expected to be of the form "Pos<n>"' % pos_dir_name
print('micro_manager_metadata_file_parent_path = %s' % micro_manager_metadata_file_parent_path) print('micro_manager_metadata_file_parent_path = %s' % micro_manager_metadata_file_parent_path)
dac_file_path = micro_manager_metadata_file_parent_path + '/display_and_comments.txt' dac_file_path = os.path.join(micro_manager_metadata_file_parent_path, 'display_and_comments.txt')
dac_id = '/'.join(self.sequence_id.split('/')[0:-1]) (dac_id, file_name) = os.path.split(self.sequence_id)
self.dac = DacMetadata(dac_id, dac_file_path) self.dac = DacMetadata(dac_id, dac_file_path)
for channel_index in range(self.num_channels): for channel_index in range(self.num_channels):
@ -74,7 +81,8 @@ class Sequence(object):
return int(summary['BitDepth']) return int(summary['BitDepth'])
def get_root_path(self): def get_root_path(self):
return '/'.join(self.micro_manager_metadata_file_path.split('/')[:-1]) (dir_name, file_name) = os.path.split(self.micro_manager_metadata_file_path) # pylint: disable=unused-variable
return dir_name
def get_image_file_path(self, channel_index, frame_index, slice_index=0): def get_image_file_path(self, channel_index, frame_index, slice_index=0):
''' '''
@ -86,7 +94,7 @@ class Sequence(object):
assert channel_index < self.num_channels assert channel_index < self.num_channels
frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, slice_index)] frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, slice_index)]
rel_file_path = frame_info['FileName'] rel_file_path = frame_info['FileName']
return self.get_root_path() + '/' + rel_file_path return os.path.join(self.get_root_path(), rel_file_path)
def get_channel_index(self, channel_id): def get_channel_index(self, channel_id):
''' '''
@ -175,11 +183,11 @@ class ImageCatalog(object):
self.sequences = {} self.sequences = {}
sequence_paths = find_dirs_containing_file('metadata.txt', self.raw_images_root) sequence_paths = find_dirs_containing_file('metadata.txt', self.raw_images_root)
sequence_ids = [ sequence_path.replace(raw_images_root+'/', '') for sequence_path in sequence_paths ] sequence_ids = [ os.path.relpath(sequence_path, raw_images_root) for sequence_path in sequence_paths ]
# nb : we use the path as sequence id because the "Comment" field in the summary section of the metadata file is not guaranteed to be unique (eg they are the same in res_soleil2018/white/white_24112018_1/Pos0 and in res_soleil2018/white/white_24112018_2/Pos0) # nb : we use the path as sequence id because the "Comment" field in the summary section of the metadata file is not guaranteed to be unique (eg they are the same in res_soleil2018/white/white_24112018_1/Pos0 and in res_soleil2018/white/white_24112018_2/Pos0)
for sequence_id in sequence_ids: for sequence_id in sequence_ids:
micro_manager_metadata_file_path = raw_images_root + '/' + sequence_id + '/metadata.txt' micro_manager_metadata_file_path = os.path.join(raw_images_root, sequence_id, 'metadata.txt')
# micro_manager_metadata_file_path = '/tmp/toto.json' # micro_manager_metadata_file_path = '/tmp/toto.json'
self.sequences[sequence_id] = Sequence(self, sequence_id, micro_manager_metadata_file_path) self.sequences[sequence_id] = Sequence(self, sequence_id, micro_manager_metadata_file_path)

10
src/lipase/settings.py
View File

@ -1,6 +1,8 @@
"""Lipase user settings.""" """Lipase user settings."""
import json import json
from os.path import expanduser #from os.path import expanduser
#import os.path
import os
class UserSettings(object): class UserSettings(object):
@ -39,8 +41,8 @@ class UserSettings(object):
def get_settings_file_path(self): def get_settings_file_path(self):
"""Return the location of lipase user settings file.""" """Return the location of lipase user settings file."""
home = expanduser("~") home = os.path.expanduser("~")
return '%s/.fr.univ-rennes1.ipr.lipase.json' % home return os.path.join(home, '.fr.univ-rennes1.ipr.lipase.json')
def save(self): def save(self):
"""Save user settings.""" """Save user settings."""
@ -52,7 +54,7 @@ def test():
"""Unit test.""" """Unit test."""
settings = UserSettings() settings = UserSettings()
print(settings.raw_images_root_path) print(settings.raw_images_root_path)
settings.raw_images_root_path = '/Users/graffy/ownCloud/ipr/lipase/raw-images' settings.raw_images_root_path = os.path.join(os.sep, 'Users', 'graffy', 'ownCloud', 'ipr', 'lipase', 'raw-images')
# settings.toto = 'hello' # settings.toto = 'hello'
settings.save() settings.save()