Split Dataset XML generation

Rhapso/data_prep/xml_to_dataframe.py

@@ -18,8 +18,16 @@ def parse_image_loader_zarr(self, root):
         for il in root.findall(".//ImageLoader/zgroups/zgroup"):
             view_setup = il.get("setup")
             timepoint = il.get("timepoint")
-            file_path = il.find("path").text if il.find("path") is not None else None
-            channel = file_path.split("_ch_", 1)[1].split(".ome.zarr", 1)[0]
+            file_path = il.get("path")
+            if file_path is None:
+                element_string = ET.tostring(il, encoding='unicode')
+                raise ValueError(f"zgroup element missing 'path' attribute: {element_string}")
+
+            # default to channel 0 if not parseable from the path name
+            try:
+                channel = file_path.split("_ch_", 1)[1].split(".ome.zarr", 1)[0]
+            except (IndexError, AttributeError):
+                channel = 0
 
             image_loader_data.append(
                 {

Rhapso/detection/advanced_refinement.py

@@ -163,7 +163,9 @@ def filter(self):
                 lb = row['lower_bound']
                 ub = row['upper_bound']
                 if vid == view_id:
-                    to_process_interval = (lb, ub)
+
+                    ub_inclusive = (ub[0]+1, ub[1]+1, ub[2]+1)
+                    to_process_interval = (lb, ub_inclusive)
                     ips_block = []
                     intensities_block = []
 

Rhapso/detection/overlap_detection.py

@@ -5,6 +5,7 @@
 import s3fs
 import dask.array as da
 import math
+import os
 
 """
 Overlap Detection figures out where image tile overlap. 
@@ -50,7 +51,7 @@ def load_image_metadata(self, file_path):
             return self.image_shape_cache[file_path]
 
         if self.file_type == 'zarr':
-            s3 = s3fs.S3FileSystem(anon=False)
+            s3 = s3fs.S3FileSystem(anon=True)
             store = s3fs.S3Map(root=file_path, s3=s3)
             zarr_array = zarr.open(store, mode='r')
             dask_array = da.from_zarr(zarr_array)
@@ -246,7 +247,8 @@ def find_overlapping_area(self):
             all_intervals = []        
             if self.file_type == 'zarr':
                 level, leftovers = self.choose_zarr_level()
-                dim_base = self.load_image_metadata(self.prefix + row_i['file_path'] + f'/{0}')
+
+                dim_base = self.load_image_metadata(os.path.join(self.prefix, row_i['file_path']))
 
                 # isotropic pyramid
                 s = float(2 ** level)  
@@ -256,7 +258,7 @@ def find_overlapping_area(self):
                 _, dsxy, dsz = leftovers
 
             elif self.file_type == 'tiff':
-                dim_base = self.load_image_metadata(self.prefix + row_i['file_path'])
+                dim_base = self.load_image_metadata(os.path.join(self.prefix, row_i['file_path']))
                 mipmap_of_downsample = self.create_mipmap_transform()
                 dsxy, dsz = self.dsxy, self.dsz
                 level = None

Rhapso/split_dataset/compute_grid_rules.py

@@ -23,11 +23,10 @@ def closest_larger_long_divisible_by(self, a, b):
 
         return int(a + b - (a % b))
 
-    def find_min_step_size(self):
+    def find_min_step_size(self, lowest_resolution=(1.0, 1.0, 1.0)):
         """
         Compute the minimal integer step size per axis (X,Y,Z) that is compatible with the chosen lowest resolution
         """
-        lowest_resolution=(64.0, 64.0, 64.0)
         min_step_size = [1, 1, 1]
 
         for d, r in enumerate(lowest_resolution):

Rhapso/split_dataset/save_xml.py

@@ -575,9 +575,12 @@ def _norm_id(raw):
                 outer_timepoints = ch
                 break
         if outer_timepoints is None:
-            outer_timepoints = ET.Element('Timepoints', {'type': 'pattern'})
-            ip = ET.SubElement(outer_timepoints, 'integerpattern')
-            ip.text = "0"
+            tps = sorted({int(v['old_view'][0]) for v in self.self_definition if v['old_view'][0] is not None})
+            first_tp = str(tps[0]) if tps else "0"
+            last_tp = str(tps[-1]) if tps else "0"
+            outer_timepoints = ET.Element('Timepoints', {'type': 'range'})
+            ET.SubElement(outer_timepoints, 'first').text = first_tp
+            ET.SubElement(outer_timepoints, 'last').text = last_tp
             # place right after ViewSetups
             children = list(outer_seq)
             insert_idx = children.index(view_setups) + 1 if view_setups in children else len(children)