Add chromatin segmentation to data

data/rawdata/sbem-6dpf-1-whole-segmented-chromatin-labels.xml

+<SpimData version="0.2">
+  <BasePath type="relative">.</BasePath>
+  <SequenceDescription>
+    <ImageLoader format="bdv.hdf5">
+      <hdf5 type="relative">sbem-6dpf-1-whole-segmented-chromatin-labels.h5</hdf5>
+    </ImageLoader>
+    <ViewSetups>
+      <Attributes name="channel">
+        <Channel>
+          <id>1</id>
+          <name>1</name>
+        </Channel>
+      </Attributes>
+      <ViewSetup>
+        <id>0</id>
+        <name>channel 1</name>
+        <size>13750 12958 11416</size>
+        <voxelSize>
+          <unit>micrometer</unit>
+          <size>0.02 0.02 0.025</size>
+        </voxelSize>
+        <attributes>
+          <channel>1</channel>
+        </attributes>
+      </ViewSetup>
+    </ViewSetups>
+    <Timepoints type="range">
+      <first>0</first>
+      <last>0</last>
+    </Timepoints>
+  </SequenceDescription>
+  <ViewRegistrations>
+    <ViewRegistration setup="0" timepoint="0">
+      <ViewTransform type="affine">
+        <affine>0.02 0.0 0.0 0.0 0.0 0.02 0.0 0.0 0.0 0.0 0.025 0.0</affine>
+      </ViewTransform>
+    </ViewRegistration>
+  </ViewRegistrations>
+</SpimData>

make_initial_version.py

@@ -8,6 +8,7 @@ import h5py
 from scripts.files import make_folder_structure
 from scripts.export import export_segmentation
 from scripts.files import make_bdv_server_file, copy_image_data, copy_misc_data
+from scripts.files import copy_segmentation
 from scripts.attributes import make_nucleus_tables, make_cell_tables
 from pybdv.converter import make_bdv
 
@@ -71,6 +72,18 @@ def make_prospr_region_segmentations():
                  unit='micrometer', resolution=[0.5, 0.5, 0.5])
 
 
+def insert_chromatin():
+    src_folder = 'data/rawdata'
+    dst_folder = 'data/0.2.0'
+    name = 'sbem-6dpf-1-whole-segmented-chromatin-labels'
+    copy_segmentation(src_folder, dst_folder, name)
+    src_table = '/g/arendt/EM_6dpf_segmentation/EM-Prospr/tables/em-segmented-chromatin-labels.csv'
+    dst_table = os.path.join(dst_folder, 'tables', name)
+    os.makedirs(dst_table, exist_ok=True)
+    dst_table = os.path.join(dst_table, 'base.csv')
+    copyfile(src_table, dst_table)
+
+
 def make_initial_version():
 
     src_folder = 'data/rawdata'
@@ -96,7 +109,7 @@ def make_initial_version():
                          os.path.join(folder, 'misc', 'bdvserver.txt'))
 
 
-
 if __name__ == '__main__':
+    insert_chromatin()
     # make_prospr_region_segmentations()
-    make_initial_version()
+    # make_initial_version()

update_platy_browser.py

@@ -102,8 +102,11 @@ def export_segmentations(folder, new_folder,
         copy_segmentation(folder, new_folder, NAME_CILIA)
 
     # copy static segmentations
+    # we also treat the chromatin segmentation as static for now,
+    # but might change this at some point
     static_seg_names = ('sbem-6dpf-1-whole-segmented-muscles',
-                        'sbem-6dpf-1-whole-segmented-tissue-labels')
+                        'sbem-6dpf-1-whole-segmented-tissue-labels',
+                        'sbem-6dpf-1-whole-segmented-chromatin-labels')
     for seg_name in static_seg_names:
         copy_segmentation(folder, new_folder, seg_name)
 
@@ -134,7 +137,8 @@ def make_attributes(folder, new_folder,
         copy_tables(folder, new_folder, NAME_CILIA)
 
     # copy tables associated with static segmentations
-    static_seg_names = ('sbem-6dpf-1-whole-segmented-tissue-labels',)
+    static_seg_names = ('sbem-6dpf-1-whole-segmented-tissue-labels',
+                        'sbem-6dpf-1-whole-segmented-chromatin-labels')
     for seg_name in static_seg_names:
         copy_tables(folder, new_folder, seg_name)
 
@@ -198,7 +202,10 @@ def update_platy_browser(update_cell_segmentation=False,
                                update_cell_tables,
                                update_nucleus_tables,
                                update_cilia_tables)
-    if not update_dict['have_changes']:
+
+    # if an explicit tag was given, we force an update
+    force_update = new_tag != ''
+    if not update_dict['have_changes'] and not force_update:
         print("Nothing needs to be update, skipping")
         return
 
@@ -240,6 +247,8 @@ def update_platy_browser(update_cell_segmentation=False,
                     update_cilia_tables,
                     target=target, max_jobs=max_jobs)
 
+    # TODO add some quality control that cheks that all files are there
+
     # TODO implement make release properly
     return
     # make new release