ome schema finished

SchapiroLabor · Sep 27, 2024 · 8780eb3 · 8780eb3
1 parent 3ef3f73
commit 8780eb3
Show file tree

Hide file tree

Showing 3 changed files with 30 additions and 44 deletions.
diff --git a/macsima2mc/macsima2mc.py b/macsima2mc/macsima2mc.py
@@ -5,7 +5,8 @@
 import os
 
 
-input_test_folder=Path("D:/macsima_data_samples/macsima_data_v2/6_Cycle1")
+
+input_test_folder=Path("D:/macsima_data_samples/macsima_data_v2/8_Cycle2")
 output_test_folder=Path('D:/test_folder')
 
 info=helpers.cycle_info(input_test_folder, macsima_pattern(version=2),ref_marker= 'DAPI')

diff --git a/macsima2mc/ome_schema.py b/macsima2mc/ome_schema.py
@@ -27,7 +27,7 @@ def INPUTS(frame,conformed_markers):
 
 
 
-def TIFF_block(no_of_channels,
+def TIFF_array(no_of_channels,
                 inputs={'offset':0}
                 ):
 
@@ -42,7 +42,7 @@ def TIFF_block(no_of_channels,
 
     return TIFF
 
-def PLANE_block(no_of_channels,inputs):
+def PLANE_array(no_of_channels,inputs):
 
     PLANE=[
         Plane(
@@ -61,7 +61,7 @@ def PLANE_block(no_of_channels,inputs):
 
     return PLANE
 
-def CHANN_block(no_of_channels,inputs):
+def CHANN_array(no_of_channels,inputs):
 
     CHANN=[
         Channel(
@@ -78,7 +78,7 @@ def CHANN_block(no_of_channels,inputs):
 
     return CHANN
 
-def PIXELS_block(chann_block,plane_block,tiff_block,inputs):
+def PIXELS_array(chann_block,plane_block,tiff_block,inputs):
 
     PIXELS=[
         Pixels(
@@ -106,21 +106,18 @@ def PIXELS_block(chann_block,plane_block,tiff_block,inputs):
 
     return PIXELS
 
-def IMAGE_block(no_of_tiles,
-                inputs={'pix_block':[]}
-                ):
+def IMAGE_array(pixels_block,imageID):
 
     IMAGE=[
         Image(
-            id=ome_types.model.simple_types.ImageID('Image:{x}'.format(x=t)),
-            pixels=inputs['pix_block'][t]
+            id=ome_types.model.simple_types.ImageID('Image:{x}'.format(x=imageID)),
+            pixels=pixels_block
             )
-            for t in range(0,no_of_tiles)
-            ]
+        ]
 
     return IMAGE
 
-def OME_xml(inputs={'img_block':[]}):
+def OME_xml(image_block):
 
     ome=OME()
     ome.creator=" ".join([ome_types.__name__,
@@ -129,7 +126,7 @@ def OME_xml(inputs={'img_block':[]}):
                         platform.python_version()
                         ]
                         )
-    ome.images=inputs['img_block']
+    ome.images=image_block
     ome.uuid=uuid4().urn
     ome_xml=to_xml(ome)
 

diff --git a/macsima2mc/ome_writer.py b/macsima2mc/ome_writer.py
@@ -12,35 +12,23 @@
 def create_ome(tile_info,conformed_markers):
     grouped_tiles=tile_info.groupby(['tile'])
     no_of_channels=len(conformed_markers)
-
+    tiles_counter=0
+    image=[]
     for tileID,frame in grouped_tiles:
-        for marker,filter in conformed_markers:
-                metadata=frame.loc[ (frame['marker']==marker) & (frame['filter']==filter) ]
-                metadata.position_x.values[0]
-
-
-        tiff=schema.TIFF_block(no_of_channels,
-            inputs={'offset':n*no_of_channels}
-            )
-        plane=schema.PLANE_block(no_of_channels,
-            inputs={'position_x':0,'position_x_unit':'','position_y':0,'position_y_unit':'','exposure_time':[]}
-            )
-        ch=schema.CHANN_block()
-
-
-        a=[schema.IMAGE_block(
-
-            schema.PIXELS_block( inputs={'tile_id':0,'size_x':0,'size_y':0,'type':'',
-                        'chann_block':[],'pix_size_x':0,'pix_size_y':0,
-                        'pix_size_x_units':'','pix_size_y_units':'',
-                        'plane_block':[],'sig_bits':0,'tiff_block':[]
-                        }
-
-            }
-
-            )
-
-
-        )]
-
+        metadata=schema.INPUTS(frame, conformed_markers)
+        tiff=schema.TIFF_array( no_of_channels, inputs={'offset':no_of_channels*tiles_counter} )
+        plane=schema.PLANE_array(no_of_channels, metadata)
+        channel=schema.CHANN_array(no_of_channels,metadata)
+        image.append( schema.IMAGE_array ( 
+            schema.PIXELS_array(channel,plane,tiff,metadata),
+             tiles_counter 
+             ) 
+             )
+        tiles_counter=+1
+
+    ome_xml=schema.OME_xml(image)
+
+    return ome_xml
+
+