Fix some path issues and error handling in bdv script

data/0.3.0/images/prospr-6dpf-1-whole-ref-SPM.xml

@@ -2,7 +2,7 @@
   <BasePath type="relative">.</BasePath>
   <SequenceDescription>
     <ImageLoader format="bdv.hdf5">
-      <hdf5 type="relative">../rawdata/prospr-6dpf-1-whole-ref-SPM.h5</hdf5>
+        <hdf5 type="relative">../../rawdata/prospr-6dpf-1-whole-ref-SPM.h5</hdf5>
     </ImageLoader>
     <ViewSetups>
       <ViewSetup>

data/0.3.0/misc/bdv_server.txt

@@ -207,9 +207,12 @@ prospr-6dpf-1-whole-segmented-RestOfAnimal	../images/prospr-6dpf-1-whole-segment
 prospr-6dpf-1-whole-segmented-Stomodeum	../images/prospr-6dpf-1-whole-segmented-Stomodeum.xml
 prospr-6dpf-1-whole-segmented-VNC	../images/prospr-6dpf-1-whole-segmented-VNC.xml
 prospr-6dpf-1-whole-six12-MED	../images/prospr-6dpf-1-whole-six12-MED.xml
+prospr-6dpf-1-whole-ref-SPM	../images/prospr-6dpf-1-whole-ref-SPM.xml
 sbem-6dpf-1-whole-segmented-chromatin-labels	../segmentations/sbem-6dpf-1-whole-segmented-chromatin-labels.xml
 sbem-6dpf-1-whole-segmented-tissue-labels	../segmentations/sbem-6dpf-1-whole-segmented-tissue-labels.xml
 sbem-6dpf-1-whole-segmented-muscle	../segmentations/sbem-6dpf-1-whole-segmented-muscle.xml
 sbem-6dpf-1-whole-segmented-cells-labels	../segmentations/sbem-6dpf-1-whole-segmented-cells-labels.xml
 sbem-6dpf-1-whole-segmented-nuclei-labels	../segmentations/sbem-6dpf-1-whole-segmented-nuclei-labels.xml
 sbem-6dpf-1-whole-segmented-cilia-labels	../segmentations/sbem-6dpf-1-whole-segmented-cilia-labels.xml
+sbem-6dpf-1-whole-segmented-ariande-neuropil	../segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml
+sbem-6dpf-1-whole-segmented-cats-neuropil	../segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml

data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-ariande-neuropil.xml

@@ -2,7 +2,7 @@
   <BasePath type="relative">.</BasePath>
   <SequenceDescription>
     <ImageLoader format="bdv.hdf5">
-      <hdf5 type="relative">../rawdata/sbem-6dpf-1-whole-segmented-ariande-neuropil.h5</hdf5>
+        <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-segmented-ariande-neuropil.h5</hdf5>
     </ImageLoader>
     <ViewSetups>
       <ViewSetup>

data/0.3.0/segmentations/sbem-6dpf-1-whole-segmented-cats-neuropil.xml

@@ -2,7 +2,7 @@
   <BasePath type="relative">.</BasePath>
   <SequenceDescription>
     <ImageLoader format="bdv.hdf5">
-      <hdf5 type="relative">../rawdata/sbem-6dpf-1-whole-segmented-cats-neuropil.h5</hdf5>
+        <hdf5 type="relative">../../rawdata/sbem-6dpf-1-whole-segmented-cats-neuropil.h5</hdf5>
     </ImageLoader>
     <ViewSetups>
       <ViewSetup>

scripts/files/bdv_server.py

@@ -9,11 +9,12 @@ def add_to_bdv_config(name, path, bdv_config, relative_paths, ref_dir):
     h5path = get_h5_path_from_xml(path, return_absolute_path=True)
     if not os.path.exists(h5path):
         msg = 'Path to h5-file in xml does not exist - %s, %s' % (path, h5path)
-        return RuntimeError(msg)
+        raise RuntimeError(msg)
 
     if relative_paths:
         path = os.path.relpath(path, ref_dir)
     bdv_config[name] = path
+    return bdv_config
 
 
 def make_bdv_server_file(folder, out_path, relative_paths=True):
@@ -29,13 +30,15 @@ def make_bdv_server_file(folder, out_path, relative_paths=True):
         if name in privates:
             continue
         path = os.path.join(folder, 'images', '%s.xml' % name)
-        add_to_bdv_config(name, path, bdv_config, relative_paths, ref_dir)
+        bdv_config = add_to_bdv_config(name, path, bdv_config,
+                                       relative_paths, ref_dir)
 
     for name in seg_names:
         if name in privates:
             continue
         path = os.path.join(folder, 'segmentations', '%s.xml' % name)
-        add_to_bdv_config(name, path, bdv_config, relative_paths, ref_dir)
+        bdv_config = add_to_bdv_config(name, path, bdv_config,
+                                       relative_paths, ref_dir)
 
     with open(out_path, 'w') as f:
         for name, path in bdv_config.items():

scripts/files/copy_helper.py

@@ -4,6 +4,7 @@ from .xml_utils import copy_xml_with_newpath, get_h5_path_from_xml
 from .sources import get_image_names, get_segmentation_names, get_segmentations
 
 
+# TODO double check this
 def copy_file(xml_in, xml_out):
     h5path = get_h5_path_from_xml(xml_in, return_absolute_path=True)
     xml_dir = os.path.split(xml_out)[0]