started the development of imagej scripts to process the images captures on soleil platform

At this stage, the script is able to load and duisplay a sequence as an 
imageJ hyperstack

lipase.py

@@ -0,0 +1,134 @@
+# 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()