Remove splitting

Decided burden of preparing the data on the end user. Fiji can be used to crop the image to make processing faster, split it to only include one laser pass and to bin it if denoising is required. However, I will keep the h5 reader as part of this plugin to make the conversion from h5 to tif easier.

src/napari_melt_pool_tracker/_tests/test_widget.py

@@ -16,28 +16,24 @@ def test_example_q_widget(make_napari_viewer, capsys):
     widget = MeltPoolTrackerQWidget(viewer)
 
     # test widget methods
-    widget.split_groupbox.comboboxs["Input"].setCurrentText("test_image")
-    widget._split()
-    widget.speed_pos_groupbox.comboboxs["Input"].setCurrentText("test_image_0")
+    widget.speed_pos_groupbox.comboboxs["Input"].setCurrentText("test_image")
     widget._determine_laser_speed_and_position()
-    widget.window_groupbox.comboboxs["Stack"].setCurrentText("test_image_0")
-    widget.window_groupbox.comboboxs["Line"].setCurrentText(
-        "test_image_0_line"
-    )
+    widget.window_groupbox.comboboxs["Stack"].setCurrentText("test_image")
+    widget.window_groupbox.comboboxs["Line"].setCurrentText("test_image_line")
     widget._reslice_with_moving_window()
     widget.filter_groupbox.comboboxs["Input"].setCurrentText(
-        "test_image_0_resliced"
+        "test_image_resliced"
     )
     widget._filter()
     widget.radial_groupbox.comboboxs["Input"].setCurrentText(
-        "test_image_0_resliced_filtered"
+        "test_image_resliced_filtered"
     )
     widget._calculate_radial_gradient()
     widget.annotate_surface_groupbox.comboboxs["Input"].setCurrentText(
-        "test_image_0_resliced_filtered_radial_gradient"
+        "test_image_resliced_filtered_radial_gradient"
     )
     widget.annotate_surface_groupbox.comboboxs["Surface"].setCurrentText(
-        "test_image_0_resliced_filtered"
+        "test_image_resliced_filtered"
     )
     widget._annotate_surface_features()
 

src/napari_melt_pool_tracker/_widget.py

@@ -83,23 +83,11 @@ def __init__(self, napari_viewer):
         self.viewer = napari_viewer
         self.comboboxs = []
 
-        #####################
-        # Spliting
-        #####################
-        self.split_groupbox = StepWidget(name="1. Split")
-        self.split_groupbox.btn.clicked.connect(self._split)
-        self._populate_combobox(
-            self.split_groupbox.comboboxs["Input"], "image"
-        )
-        self.comboboxs.append(
-            (self.split_groupbox.comboboxs["Input"], "image")
-        )
-
         #####################
         # Laser position
         #####################
         self.speed_pos_groupbox = StepWidget(
-            name="2. Determine laser speed and position",
+            name="1. Determine laser speed and position",
         )
         self.speed_pos_groupbox.btn.clicked.connect(
             self._determine_laser_speed_and_position
@@ -115,7 +103,7 @@ def __init__(self, napari_viewer):
         # Reslice
         #####################
         self.window_groupbox = StepWidget(
-            name="3. Reslice with moving window",
+            name="2. Reslice with moving window",
             include_auto_run_and_overwrite=True,
             comboboxs=["Stack", "Line"],
             sliders={
@@ -148,7 +136,7 @@ def __init__(self, napari_viewer):
         # Denoise image
         #####################
         self.filter_groupbox = StepWidget(
-            name="4. Filter image",
+            name="3. Filter image",
             include_auto_run_and_overwrite=True,
             sliders={
                 "Kernel t": (1, 15, 7),
@@ -172,7 +160,7 @@ def __init__(self, napari_viewer):
         #####################
         # Radial gradient
         #####################
-        self.radial_groupbox = StepWidget(name="5. Calculate radial gradient")
+        self.radial_groupbox = StepWidget(name="4. Calculate radial gradient")
         self.radial_groupbox.btn.clicked.connect(
             self._calculate_radial_gradient
         )
@@ -187,7 +175,7 @@ def __init__(self, napari_viewer):
         # Surface annotation
         #####################
         self.annotate_surface_groupbox = StepWidget(
-            name="6. Annotate surface features",
+            name="5. Annotate surface features",
             comboboxs=["Input", "Surface"],
         )
         self.annotate_surface_groupbox.btn.clicked.connect(
@@ -209,7 +197,7 @@ def __init__(self, napari_viewer):
         #####################
         # Depth annotation
         #####################
-        annotate_depth_groupbox = QGroupBox("7. Annotate depths")
+        annotate_depth_groupbox = QGroupBox("6. Annotate depths")
         annotate_depth_layout = QVBoxLayout()
         annotate_depth_groupbox.setLayout(annotate_depth_layout)
         annotate_depth_layout.addWidget(
@@ -229,7 +217,6 @@ def __init__(self, napari_viewer):
         self.scroll_content.setLayout(self.scroll_layout)
 
         # Add individual widges to plugin
-        self.scroll_layout.addWidget(self.split_groupbox)
         self.scroll_layout.addWidget(self.speed_pos_groupbox)
         self.scroll_layout.addWidget(self.window_groupbox)
         self.scroll_layout.addWidget(self.filter_groupbox)
@@ -244,24 +231,6 @@ def __init__(self, napari_viewer):
 
         self.parameters = {}
 
-    def _split(self):
-        selected_layers = self.viewer.layers.selection
-        t = self.viewer.dims.current_step[0]
-        self.parameters["split_t"] = t
-        layer = selected_layers.pop()
-        data, meta, layer_type = layer.as_layer_data_tuple()
-        if layer_type != "image":
-            raise ValueError(
-                "Can only split image layers. You have selected a layer of type {layer_type}."
-            )
-        data0 = data[:t]
-        data1 = data[t:]
-        name = meta["name"]
-        meta["name"] = name + "_0"
-        self.viewer.add_image(data0, **meta)
-        meta["name"] = name + "_1"
-        self.viewer.add_image(data1, **meta)
-
     def _determine_laser_speed_and_position(self):
         name = self.speed_pos_groupbox.comboboxs["Input"].currentText()
         layer_names = [