Rhapso 0.2.1__py3-none-any.whl → 0.2.2__py3-none-any.whl

Rhapso/matching/ransac_matching.py

@@ -271,7 +271,7 @@ class RansacMatching:
             for b in range(1):
 
                 matches = []
-                for i in range(3):
+                for i in range(self.num_required_neighbors):
                     point_match = (desc_a['relative_descriptors'][i], desc_b['relative_descriptors'][i])
                     matches.append(point_match)
 

Rhapso/pipelines/ray/local/alignment_pipeline.py

@@ -9,7 +9,7 @@ import ray
 ray.init()
 
 # Point to param file
-with open("Rhapso/pipelines/ray/param/exaSPIM_802450.yml", "r") as file:
+with open("Rhapso/pipelines/ray/param/exaSPIM_794495.yml", "r") as file:
     config = yaml.safe_load(file)
 
 # -- INITIALIZE EACH COMPONENT --

Rhapso/split_dataset/save_xml.py

@@ -13,13 +13,6 @@ class SaveXML:
         self.xml_output_path = xml_output_path
     
     def save_tile_attributes_to_xml(self, xml):
-        """
-        Ensure the *last* <ViewSetups> (the outer split one) has:
-        - <Attributes name="illumination"> old_tile_0..N </Attributes>
-        - <Attributes name="channel"> ... </Attributes>
-        - <Attributes name="tile"> with locations from Image Splitting </Attributes>
-        - <Attributes name="angle"><Angle id=0 name=0/></Attributes>
-        """
         root = ET.fromstring(xml)
 
         def tagname(el):
@@ -249,26 +242,6 @@ class SaveXML:
         """
         Wrap the top-level ImageLoader in <ImageLoader format="split.viewerimgloader">
         and move the ORIGINAL ViewSetups/Timepoints/MissingViews into an inner
-        <SequenceDescription> inside that wrapper.
-
-        Resulting structure:
-
-        <SpimData>
-          <BasePath/>
-          <SequenceDescription>
-            <ImageLoader format="split.viewerimgloader">
-              <ImageLoader format="bdv.multimg.zarr"> ... </ImageLoader>
-              <SequenceDescription>
-                <ViewSetups>  (ORIGINAL)  </ViewSetups>
-                <Timepoints>  (ORIGINAL)  </Timepoints>
-                <MissingViews/>
-              </SequenceDescription>
-              <!-- SetupIds (for split tiles) will be added later -->
-            </ImageLoader>
-            <!-- NEW ViewSetups/Timepoints/MissingViews for split views are added later -->
-          </SequenceDescription>
-          <ViewRegistrations> ... </ViewRegistrations>
-        </SpimData>
         """
         root = ET.fromstring(xml)
 
@@ -309,8 +282,6 @@ class SaveXML:
         if fmt == 'split.viewerimgloader':
             return xml
 
-        # Collect any other ImageLoader siblings (other sources)
-        other_imageloaders = []
         # Collect ORIGINAL ViewSetups / Timepoints / MissingViews that are siblings
         orig_viewsetups = None
         orig_timepoints = None
@@ -318,18 +289,15 @@ class SaveXML:
 
         for ch in children[base_loader_idx + 1:]:
             name = tn(ch)
-            if name == 'ImageLoader':
-                other_imageloaders.append(ch)
-            elif name == 'ViewSetups':
+            if name == 'ViewSetups':
                 orig_viewsetups = ch
             elif name == 'Timepoints':
                 orig_timepoints = ch
             elif name == 'MissingViews':
                 orig_missingviews = ch
-            
 
         # Remove them from the outer SequenceDescription
-        for node in (orig_viewsetups, orig_timepoints, orig_missingviews, *other_imageloaders):
+        for node in (orig_viewsetups, orig_timepoints, orig_missingviews):
             if node is not None and node in seq:
                 seq.remove(node)
 
@@ -340,12 +308,9 @@ class SaveXML:
         wrapper = ET.Element('ImageLoader', {'format': 'split.viewerimgloader'})
         # First child: original loader
         wrapper.append(base_loader)
-        for other_loader in other_imageloaders:
-            wrapper.append(other_loader)
 
         # Inner <SequenceDescription> that holds the original ViewSetups/Timepoints/MissingViews
         inner_seq = ET.Element('SequenceDescription')
-
         if orig_viewsetups is not None:
             inner_seq.append(orig_viewsetups)
         if orig_timepoints is not None:
@@ -516,33 +481,6 @@ class SaveXML:
         return ET.tostring(root, encoding='unicode')
 
     def save_setup_id_to_xml(self, xml):
-        """
-        Create/overwrite the OUTER <ViewSetups> (split tiles) and ensure outer
-        <Timepoints> and <MissingViews> exist under the top-level SequenceDescription.
-
-        Outer layout target:
-
-        <SpimData>
-          <BasePath/>
-          <SequenceDescription>
-            <ImageLoader format="split.viewerimgloader">
-              ...
-              <SequenceDescription>  (original)  </SequenceDescription>
-              <SetupIds> ... </SetupIds>        (from save_setup_id_definition_to_xml)
-            </ImageLoader>
-            <ViewSetups>            <-- created here (ids 0..499)
-              <ViewSetup>...</ViewSetup>
-              ...
-              <Attributes ...>...</Attributes>
-            </ViewSetups>
-            <Timepoints type="pattern">
-              <integerpattern>0</integerpattern>
-            </Timepoints>
-            <MissingViews/>
-          </SequenceDescription>
-          <ViewRegistrations>...</ViewRegistrations>
-        </SpimData>
-        """
         root = ET.fromstring(xml)
 
         def tn(el):

{rhapso-0.2.1.dist-info → rhapso-0.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: Rhapso
-Version: 0.2.1
+Version: 0.2.2
 Summary: A python package for aligning and stitching light sheet fluorescence microscopy images
 Author: ND
 Author-email: sean.fite@alleninstitute.org

{rhapso-0.2.1.dist-info → rhapso-0.2.2.dist-info}/RECORD

@@ -56,7 +56,7 @@ Rhapso/fusion/neuroglancer_link_gen/utils/transfer.py,sha256=8hFBM8lmCV3TsEEVXZk
 Rhapso/fusion/neuroglancer_link_gen/utils/utils.py,sha256=Q0jKPGI39ScCHDgVEoWbrZrBrEluCjm69z28T3JScTc,7322
 Rhapso/matching/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 Rhapso/matching/load_and_transform_points.py,sha256=UEV9gnWyl2z4zAUR2Z_ewX1_TWoS-IpXPL-qRB1_Ms8,16416
-Rhapso/matching/ransac_matching.py,sha256=BWSRmckG2GiA49RuGnja4le-Xo5o9aY53Yawes9P-_E,20268
+Rhapso/matching/ransac_matching.py,sha256=H5El2x-sw2snbOZVsbmo2fX-F3i9g3Xd-nNz1Z2UT48,20294
 Rhapso/matching/save_matches.py,sha256=OYHzzGoF9-PTVfQZBJ7HaJ9JYB_Q8ZazH-f3HljxzLQ,4720
 Rhapso/matching/xml_parser.py,sha256=nP_jA_jEfAFPzt6Al91NpwWEk-Klk8P5QzNINJYVksU,11527
 Rhapso/pipelines/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -71,7 +71,7 @@ Rhapso/pipelines/ray/aws/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZ
 Rhapso/pipelines/ray/aws/alignment_pipeline.py,sha256=c_UUw_90xnoAJ5zYuU5OD0Uzr1cPOqsZ6aXHOQauYCI,10015
 Rhapso/pipelines/ray/aws/config/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 Rhapso/pipelines/ray/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-Rhapso/pipelines/ray/local/alignment_pipeline.py,sha256=EV2e0Kfx7uSHaIVMTKId-NG8f6B4TCWnI5yqSRrmuFE,6989
+Rhapso/pipelines/ray/local/alignment_pipeline.py,sha256=lhk9Xx8d3wQctxi834OlB8vQelwvVCqs-WKKQxtEVtU,6989
 Rhapso/pipelines/ray/param/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 Rhapso/solver/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 Rhapso/solver/compute_tiles.py,sha256=-7QFrZZfh1iW1nDdlBORlcqOGf7urJmgjWOj6DfDdHQ,20471
@@ -87,15 +87,15 @@ Rhapso/solver/xml_to_dataframe_solver.py,sha256=u96DPnZNDa-TgimsPqyZlIvHk4A1e8yZ
 Rhapso/split_dataset/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 Rhapso/split_dataset/compute_grid_rules.py,sha256=dCAuNs4D7SaCfTXp54lchgttZVSgLH5f1tQWtkwr_ws,3028
 Rhapso/split_dataset/save_points.py,sha256=k-jH-slmxkbrxDl-uJvDkwOedi6cg7md3kg_a0NdL24,3713
-Rhapso/split_dataset/save_xml.py,sha256=55NdzfHPGAhpR1QYaDwXPZQlZlP6T9fymhJaOwTuZh0,29561
+Rhapso/split_dataset/save_xml.py,sha256=iVH8aEffD6ya15CIugAb9kiJsz5GTo0HKu_xz3jbnrk,27082
 Rhapso/split_dataset/split_images.py,sha256=2RzAi0btV1tmh4le9QotRif1IYUU6_4pLcGGpFBM9zk,22434
 Rhapso/split_dataset/xml_to_dataframe_split.py,sha256=ByaLzJ4sqT417UiCQU31_CS_V4Jms7pjMbBl0ZdSNNA,8570
-rhapso-0.2.1.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
+rhapso-0.2.2.dist-info/licenses/LICENSE,sha256=U0Y7B3gZJHXpjJVLgTQjM8e_c8w4JJpLgGhIdsoFR1Y,1092
 tests/__init__.py,sha256=LYf6ZGyYRcduFFSaOLmnw3rTyfS3XLib0dsTHDWH0jo,37
 tests/test_detection.py,sha256=NtFYR_du9cbKrclQcNiJYsKzyqly6ivF61pw6_NICcM,440
 tests/test_matching.py,sha256=QX0ekSdyIkPpAsXHfSMqJUUlNZg09caSlhhUM63MduM,697
 tests/test_solving.py,sha256=t8I9XPV_4ZFM-DJpgvdYXxkG2_4DQgqs-FFyE5w8Nfg,695
-rhapso-0.2.1.dist-info/METADATA,sha256=v-Js1TXvjPcxVZMwtBGL0n-9bTy69N2kbcCobgzAHTM,19319
-rhapso-0.2.1.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
-rhapso-0.2.1.dist-info/top_level.txt,sha256=NXvsrsTfdowWbM7MxEjkDZE2Jo74lmq7ruWkp70JjSw,13
-rhapso-0.2.1.dist-info/RECORD,,
+rhapso-0.2.2.dist-info/METADATA,sha256=aURyGl1kXMhJZ8bQg5BIoS3wLMy2nHX-6NOcYjbXajg,19319
+rhapso-0.2.2.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
+rhapso-0.2.2.dist-info/top_level.txt,sha256=NXvsrsTfdowWbM7MxEjkDZE2Jo74lmq7ruWkp70JjSw,13
+rhapso-0.2.2.dist-info/RECORD,,