lipase/lipase.py

# String(label="Please enter your name",description="Name field") name
# OUTPUT String greeting

# A Jython script with parameters.
# It is the duty of the scripting framework to harvest
# the 'name' parameter from the user, and then display
# the 'greeting' output parameter, based on its type.
from ij import IJ

# greeting = "Hello, " + name + "!"


# image prefix :
# AF
# blé : coupes de blé
# CA : coupe d'amande
# FE : feuille d'épinard
# GGH : globule gras humain
# CRF chloroplastes de feuille d'épinard
# OL : oléosome
# DARK : dark
# white :
#
# - cin1 : cinétique 1
#    phiG_40x_1 : cinétique avant et après injection enzyme gastrique
#    phiG_40x_Zstack20um_1 : stack
#     0mn : on commence à enregistrer et on attend 10mn (pour le bleaching) -> phiG_40x_1
#    10mn : debut injection phase gastrique (poussée)
#    13mn : la phase gastrique (le petit tuyau contient 20ul) arrive dans la cellule d'un coup (1 nanol)
#    15mn : on arrête l'injection
#    50mn : on fait un stack -> phiG_40x_Zstack20um_1
#    51mn : début d'injection phase intestinale (poussée) -> phiG_I_40x_1
#    x mn : on arrête l'injection
#    90mn : on fait un stack -> phiG_I_40x_Zstack20um_1
# - cin2 :  autre échantillon similaire à cin1
# - cond[5678] : condition non réalistes
import json

class Sequence(object):
    def __init__(self, catalog, sequence_id, micro_manager_metadata_file_path):
        self.catalog = catalog
        self.sequence_id = sequence_id
        self.micro_manager_metadata_file_path = micro_manager_metadata_file_path
        print(micro_manager_metadata_file_path)

        with open(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)
    @property
    def num_frames(self):
        summary = self.mmm['Summary']
        return int(summary['Frames'])

    @property
    def width(self):
        summary = self.mmm['Summary']
        return int(summary['Width'])

    @property
    def height(self):
        summary = self.mmm['Summary']
        return int(summary['Height'])

    @property
    def num_channels(self):
        summary = self.mmm['Summary']
        return int(summary['Channels'])

    @property
    def num_slices(self):
        summary = self.mmm['Summary']
        return int(summary['Slices'])

    @property
    def num_bits_per_pixels(self):
        summary = self.mmm['Summary']
        return int(summary['BitDepth'])

    def get_root_path(self):
        return '/'.join(self.micro_manager_metadata_file_path.split('/')[:-1])

    def get_image_file_path(self, channel_id, frame_index, z_index=0):
        assert frame_index < self.num_frames
        summary = self.mmm['Summary']
        channel_index = summary['ChNames'].index(channel_id)
        frame_info = self.mmm['FrameKey-%d-%d-%d' % (frame_index, channel_index, z_index) ]
        rel_file_path = frame_info['FileName']
        return self.get_root_path() + '/' + rel_file_path

    def open_in_imagej(self):
        #ip = IJ.createHyperStack(title=self.sequence_id, width=self.width, height= self.height, channels=1, slices=1, frames=self.get_num_frames(), bitdepth=16)
        hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, self.num_channels, self.num_slices, self.num_frames, self.num_bits_per_pixels)
        for channel_index in range(1): #self.num_channels):
            for frame_index in range(self.num_frames):
                slice_index = 0
                src_image_file_path = self.get_image_file_path(channel_id='DM300_327-353_fluo', frame_index=frame_index)
                src_image = IJ.openImage(src_image_file_path)

                hyperstack.setPosition(channel_index+1, slice_index+1, frame_index+1)
                hyperstack.setProcessor(src_image.getProcessor())
        hyperstack.show()

class ImageCatalog(object):
    def __init__(self, raw_images_root):
        self.raw_images_root = raw_images_root
        self.sequences = { }
        sequence_id = 'GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'
        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)

    def __str__(self):
        for sequence_id, sequence in self.sequences.iteritems():
            return str(sequence_id) + ':' + str(sequence)
        # self.add_micromanager_metadata(raw_images_root + '/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/metadata.txt')

    #def add_micromanager_metadata(self, micro_manager_metadata_file_path):
    #    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'
    catalog = ImageCatalog(raw_images_root)
    print(catalog)
    catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].open_in_imagej()

    #src_image_file_path = catalog.sequences['GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0'].get_image_file_path(channel_id='DM300_327-353_fluo', frame_index=3)
    #src_image = IJ.openImage(src_image_file_path)
    #dark_image = IJ.openImage(raw_images_root + '/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos0/img_000000000_DM300_327-353_fluo_000.tif')
    #src_image.show()
    #assert src_image

# If a Jython script is run, the variable __name__ contains the string '__main__'.
# If a script is loaded as module, __name__ has a different value.
if __name__ in ['__builtin__','__main__']:
    run_script()