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lipase
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Reorganised directories to ease identification of sequences. 

The sequence id now cantain the id of the image capture campaign
This commit is contained in:
Guillaume Raffy 2019-04-01 12:26:37 +02:00
parent 69abd7e660
commit 44512ba4eb
2 changed files with 15 additions and 5 deletions
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2
README.md
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@ -2,7 +2,7 @@
An image processing software suite for the project lipase (Véronique Vié, Institut de Physique de Rennes)
This software suite is developed using Fiji (an image processing package based on imageJ).
This software suite is developed as a python script for fiji (an image processing package based on imageJ).
## What it does

18
lipase.py
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@ -113,7 +113,15 @@ class ImageCatalog(object):
self.raw_images_root = raw_images_root
self.sequences = { }
for sequence_id in ['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0', 'GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']:
# 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)
sequence_ids = []
sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0')
sequence_ids.append('res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2')
sequence_ids.append('res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0')
# sequence_ids.append('res_soleil2018/white/white_24112018_1/Pos0') # this sequence seems broken (only 5 images while there's supposed to be 201 frames)
sequence_ids.append('res_soleil2018/white/white_24112018_2/Pos0')
for sequence_id in sequence_ids:
micro_manager_metadata_file_path = raw_images_root + '/' + sequence_id + '/metadata.txt'
#micro_manager_metadata_file_path = '/tmp/toto.json'
self.sequences[ sequence_id ] = Sequence(self, sequence_id, micro_manager_metadata_file_path)
@ -127,11 +135,13 @@ class ImageCatalog(object):
# self.sequences[ micro_manager_metadata_file_path ] = Sequence(self, micro_manager_metadata_file_path)
def run_script():
raw_images_root = '/Users/graffy/ownCloud/ipr/lipase/soleil-2018.test'
raw_images_root = '/Users/graffy/ownCloud/ipr/lipase/raw-images'
catalog = ImageCatalog(raw_images_root)
print(catalog)
catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].open_in_imagej()
catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'].open_in_imagej()
#catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].open_in_imagej()
catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'].open_in_imagej()
#catalog.sequences['DARK_40X_60min_1 im pae min_1/Pos0'].open_in_imagej()
#catalog.sequences['white_24112018_1/Pos0'].open_in_imagej()
if False:
sequence = catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0']