Add example of migration to ome-types for generating companion OME-XML

scripts/create_companions.py

@@ -1,7 +1,17 @@
 #!/usr/bin/env python
 import sys
-from ome_model.experimental import Plate, Image, create_companion
-import subprocess
+
+from ome_types.model import OME
+from ome_types.model import Channel
+from ome_types.model import Image
+from ome_types.model import ImageRef
+from ome_types.model import Pixels
+from ome_types.model import Plane
+from ome_types.model import Plate
+from ome_types.model import TiffData
+from ome_types.model import Well
+from ome_types.model import WellSample
+import uuid
 
 filenames = []
 with open("idr0092.files") as fp:
@@ -15,36 +25,66 @@
 rows = ['A','B','C', 'D']
 timepoints = ['0h', '24h', '48h', '72h', '96h']
 print("Creating {}.companion.ome ...".format(plate_name))
-plate = Plate(plate_name, len(rows), len(columns))
+
+ome = OME()
+plate = Plate(name=plate_name, rows=len(rows), columns=len(columns))
+ome.plates.append(plate)
+
 well_index = 0
 for row_index, row in enumerate(rows):
     for column_index, column in enumerate(columns):
-        well = plate.add_well(row_index, column_index)
+        well = Well(row=row_index, column=column_index)
+        plate.wells.append(well)
+
         test = "{}_{}{}_0h.tiff".format(plate_name, row, column)
         if test in filenames:
             basename = "{}{}".format(row, column)
-            image = Image(basename, 2080, 1552, 25, 3, len(timepoints),
-                          order="XYZTC", type="uint8")
-            image.add_channel(samplesPerPixel=3)
+            pixels = Pixels(
+                type='uint8',
+                size_x=2080,
+                size_y=1552,
+                size_z=25,
+                size_c=3,
+                size_t=len(timepoints),
+                dimension_order='XYZCT'
+            )
+            pixels.channels.append(Channel(samples_per_pixel=3))
+            image = Image(
+                name=basename,
+                pixels=pixels
+            )
+            ome.images.append(image)
+
             for i, timepoint in enumerate(timepoints):
                 filename = "{}_{}{}_{}.tiff".format(plate_name, row, column, timepoint)
-                image.add_tiff(filename, c=0, z=0, t=i, planeCount=25)
-                options = {
-                    'DeltaT': timepoint[:-1],
-                    'DeltaTUnit': 'h',
-                }
+                tiff_uuid = TiffData.UUID(
+                    value=f"urn:uuid:{uuid.uuid4()}",
+                    file_name=filename
+                    )
+                tiff = TiffData(
+                    first_c=0,
+                    first_t=i,
+                    first_z=0,
+                    plane_count=25,
+                    uuid=tiff_uuid)
+                pixels.tiff_data_blocks.append(tiff)
                 for z in range(25):
-                    image.add_plane(c=0, z=z, t=i, options=options)
-            well.add_wellsample(well_index, image)
+                    pixels.planes.append(Plane(
+                        delta_t=timepoint[:-1],
+                        delta_t_unit="h",
+                        the_c=0,
+                        the_t=i,
+                        the_z=z
+                        )
+                    )
+
+            well.well_samples.append(
+                WellSample(index=well_index, image_ref=ImageRef(id=image.id))
+            )
             well_index += 1
 companion_file = "../companions/{}.companion.ome".format(plate_name)
-create_companion(plates=[plate], out=companion_file)
-
-# Indent XML for readability
-proc = subprocess.Popen(
-    ['xmllint', '--format', '-o', companion_file, companion_file],
-    stdin=subprocess.PIPE,
-    stdout=subprocess.PIPE)
-(output, error_output) = proc.communicate()
+with open(companion_file, 'w') as f:
+    f.write(ome.to_xml())
+
 
 print("Done.")