Tile position writer now handles multi-channel images correctly

mesospim_stitcher/file_utils.py

@@ -59,7 +59,9 @@ def create_pyramid_bdv_h5(
                 yield int(100 * num_done / num_slices)
 
 
-def write_big_stitcher_tile_config(meta_file_name: Path) -> list[dict]:
+def write_big_stitcher_tile_config(
+    meta_file_name: Path, h5_path: Path
+) -> list[dict]:
     tile_metadata = parse_mesospim_metadata(meta_file_name)
 
     output_file = str(meta_file_name)[:-12] + "_tile_config.txt"
@@ -93,13 +95,19 @@ def write_big_stitcher_tile_config(meta_file_name: Path) -> list[dict]:
         )
         relative_locations.append(rel_tuple)
 
+    tile_names = []
+    with h5py.File(h5_path, "r") as f:
+        for tile in f["t00000"]:
+            tile_names.append(tile)
+
     with open(output_file, "w") as f:
         f.write("dim=3\n")
-        for i in range(len(tile_metadata)):
+        for i, tile_name in enumerate(tile_names):
+            tile_index = (i % num_channels) + (i // num_tiles) * num_channels
             f.write(
-                f"{i};;"
-                f"({relative_locations[i%num_tiles][0]},"
-                f"{relative_locations[i%num_tiles][1]},0)\n"
+                f"{tile_name[1:]};;"
+                f"({relative_locations[tile_index][0]},"
+                f"{relative_locations[tile_index][1]},0)\n"
             )
 
     return tile_metadata

mesospim_stitcher/stitching_widget.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+from typing import Dict, List
 
 import dask.array as da
 import h5py
@@ -21,6 +22,7 @@
 from mesospim_stitcher.file_utils import (
     check_mesospim_directory,
     create_pyramid_bdv_h5,
+    write_big_stitcher_tile_config,
 )
 
 DOWNSAMPLE_ARRAY = np.array(
@@ -41,7 +43,8 @@ def __init__(self, napari_viewer: Viewer):
         self.meta_path = None
         self.h5_path = None
         self.h5_file = None
-        self.tiles: da = []
+        self.tiles: List[da] = []
+        self.tile_metadata: List[Dict] = []
 
         self.setLayout(QVBoxLayout())
 
@@ -90,8 +93,13 @@ def __init__(self, napari_viewer: Viewer):
         )
         self.add_tiles_button.setEnabled(False)
         self.layout().addWidget(self.add_tiles_button)
+
         self.layout().addWidget(self.progress_bar)
 
+        self.test_button = QPushButton("Test")
+        self.test_button.clicked.connect(self._on_test_button_clicked)
+        self.layout().addWidget(self.test_button)
+
     def _on_open_file_dialog_clicked(self):
         self.working_directory = Path(
             QFileDialog.getExistingDirectory(
@@ -107,6 +115,21 @@ def _on_mesospim_directory_text_edited(self):
         )
         self.check_and_load_mesospim_directory()
 
+    def _on_create_pyramid_button_clicked(self):
+        self.progress_bar.setValue(0)
+        self.progress_bar.setRange(0, 100)
+
+        worker = create_worker(
+            create_pyramid_bdv_h5,
+            self.h5_path,
+            DOWNSAMPLE_ARRAY,
+            SUBDIVISION_ARRAY,
+            yield_progress=True,
+        )
+        worker.yielded.connect(self.progress_bar.setValue)
+        worker.finished.connect(self.progress_bar.reset)
+        worker.start()
+
     def _on_add_tiles_button_clicked(self):
         self.h5_file = h5py.File(self.h5_path, "r")
         self.tiles = []
@@ -121,34 +144,31 @@ def _on_add_tiles_button_clicked(self):
             self.tiles.append(curr_tile)
             self._viewer.add_image(
                 curr_tile,
-                contrast_limits=[0, 1500],
+                contrast_limits=[0, 2000],
                 multiscale=False,
                 name=child,
             )
 
-    def _on_create_pyramid_button_clicked(self):
-        self.progress_bar.setValue(0)
-        self.progress_bar.setRange(0, 100)
-
-        worker = create_worker(
-            create_pyramid_bdv_h5,
-            self.h5_path,
-            DOWNSAMPLE_ARRAY,
-            SUBDIVISION_ARRAY,
-            yield_progress=True,
-        )
-        worker.yielded.connect(self.progress_bar.setValue)
-        worker.finished.connect(self.progress_bar.reset)
-        worker.start()
-
     def check_and_load_mesospim_directory(self):
         try:
             (
                 self.xml_path,
                 self.meta_path,
                 self.h5_path,
             ) = check_mesospim_directory(self.working_directory)
+            with h5py.File(self.h5_path, "r") as f:
+                if len(f["t00000/s00"].keys()) <= 1:
+                    show_warning("Resolution pyramid not found")
+                    self.create_pyramid_button.setEnabled(True)
+
             self.add_tiles_button.setEnabled(True)
-            self.create_pyramid_button.setEnabled(True)
         except FileNotFoundError:
             show_warning("mesoSPIM directory not valid")
+
+    def _on_test_button_clicked(self):
+        self.tile_metadata = write_big_stitcher_tile_config(
+            self.meta_path, self.h5_path
+        )
+        print(self.tile_metadata)
+        # print([tile['x_pos'] for tile in self.tile_metadata])
+        # print([tile['y_pos'] for tile in self.tile_metadata])