Merge pull request #47 from computational-cell-analytics/45-user-interface

Add first version of user interface

Author: constantinpape

environment.yaml

@@ -8,5 +8,9 @@ dependencies:
     - pip
     - pyqt
     - magicgui
+    - pytorch
+    - bioimageio.core
+    - kornia
+    - tensorboard
     - pip:
         - napari-skimage-regionprops

setup.py

@@ -15,6 +15,9 @@
         "console_scripts": [
             "sr_tools.correct_segmentation = synaptic_reconstruction.tools.segmentation_correction:main",
             "sr_tools.measure_distances = synaptic_reconstruction.tools.distance_measurement:main",
-        ]
+        ],
+        "napari.manifest": [
+            "synaptic_reconstruction = synaptic_reconstruction:napari.yaml",
+        ],
     },
 )

synaptic_reconstruction/napari.yaml

@@ -0,0 +1,27 @@
+name: synaptic_reconstruction
+display_name: Synaptic Reconstruction
+# see https://napari.org/stable/plugins/manifest.html for valid categories
+categories: ["Image Processing", "Annotation"]
+contributions:
+  commands:
+    - id: synaptic_reconstruction.segment
+      python_name: synaptic_reconstruction.tools.synaptic_plugin.segmentation_widget:get_segmentation_widget
+      title: Segment
+    - id: synaptic_reconstruction.distance_measure
+      python_name: synaptic_reconstruction.tools.synaptic_plugin.distance_measure_widget:get_distance_measure_widget
+      title: Distance Measurement
+    - id: synaptic_reconstruction.file_reader
+      title: Read ".mrc, .rec" files
+      python_name: synaptic_reconstruction.tools.file_reader_plugin.elf_reader:get_reader
+
+  readers:
+    - command: synaptic_reconstruction.file_reader
+      filename_patterns:
+      - '*.mrc'
+      accepts_directories: false
+
+  widgets:
+    - command: synaptic_reconstruction.segment
+      display_name: Segmentation 
+    - command: synaptic_reconstruction.distance_measure
+      display_name: Distance Measurement

synaptic_reconstruction/tools/file_reader_plugin/elf_reader.py

@@ -0,0 +1,30 @@
+from typing import Callable, List, Optional, Sequence, Union
+from napari.types import LayerData
+from elf.io import open_file
+
+PathLike = str
+PathOrPaths = Union[PathLike, Sequence[PathLike]]
+ReaderFunction = Callable[[PathOrPaths], List[LayerData]]
+
+
+def get_reader(path: PathOrPaths) -> Optional[ReaderFunction]:
+    # If we recognize the format, we return the actual reader function
+    if isinstance(path, str) and path.endswith(".mrc"):
+        return elf_read_file
+    # otherwise we return None.
+    return None
+
+
+def elf_read_file(path: PathOrPaths) -> List[LayerData]:
+    try:
+        with open_file(path, mode="r") as f:
+            data = f["data"][:]
+        layer_attributes = {
+            "name": "Raw",
+            "colormap": "gray",
+            "blending": "additive"
+            }
+        return [(data, layer_attributes)]
+    except Exception as e:
+        print(f"Failed to read file: {e}")
+        return

synaptic_reconstruction/tools/synaptic_plugin/__init__.py

@@ -0,0 +1,188 @@
+from pathlib import Path
+import napari
+from qtpy.QtWidgets import QWidget, QVBoxLayout, QHBoxLayout, QPushButton, QFileDialog, QLabel, QSpinBox, QLineEdit, QGroupBox, QFormLayout, QFrame, QComboBox, QCheckBox
+import qtpy.QtWidgets as QtWidgets
+from superqt import QCollapsible
+
+
+class BaseWidget(QWidget):
+    def __init__(self):
+        super().__init__()
+        self.viewer = napari.current_viewer()
+        self.attribute_dict = {}
+
+    def _add_string_param(self, name, value, title=None, placeholder=None, layout=None, tooltip=None):
+        if layout is None:
+            layout = QtWidgets.QHBoxLayout()
+        label = QtWidgets.QLabel(title or name)
+        if tooltip:
+            label.setToolTip(tooltip)
+        layout.addWidget(label)
+        param = QtWidgets.QLineEdit()
+        param.setText(value)
+        if placeholder is not None:
+            param.setPlaceholderText(placeholder)
+        param.textChanged.connect(lambda val: setattr(self, name, val))
+        if tooltip:
+            param.setToolTip(tooltip)
+        layout.addWidget(param)
+        return param, layout
+
+    def _add_float_param(self, name, value, title=None, min_val=0.0, max_val=1.0, decimals=2,
+                         step=0.01, layout=None, tooltip=None):
+        if layout is None:
+            layout = QtWidgets.QHBoxLayout()
+        label = QtWidgets.QLabel(title or name)
+        if tooltip:
+            label.setToolTip(tooltip)
+        layout.addWidget(label)
+        param = QtWidgets.QDoubleSpinBox()
+        param.setRange(min_val, max_val)
+        param.setDecimals(decimals)
+        param.setValue(value)
+        param.setSingleStep(step)
+        param.valueChanged.connect(lambda val: setattr(self, name, val))
+        if tooltip:
+            param.setToolTip(tooltip)
+        layout.addWidget(param)
+        return param, layout
+
+    def _add_int_param(self, name, value, min_val, max_val, title=None, step=1, layout=None, tooltip=None):
+        if layout is None:
+            layout = QHBoxLayout()
+        label = QLabel(title or name)
+        if tooltip:
+            label.setToolTip(tooltip)
+        layout.addWidget(label)
+        param = QSpinBox()
+        param.setRange(min_val, max_val)
+        param.setValue(value)
+        param.setSingleStep(step)
+        param.valueChanged.connect(lambda val: setattr(self, name, val))
+        if tooltip:
+            param.setToolTip(tooltip)
+        layout.addWidget(param)
+        return param, layout
+
+    def _add_choice_param(self, name, value, options, title=None, layout=None, update=None, tooltip=None):
+        if layout is None:
+            layout = QHBoxLayout()
+        label = QLabel(title or name)
+        if tooltip:
+            label.setToolTip(tooltip)
+        layout.addWidget(label)
+
+        # Create the dropdown menu via QComboBox, set the available values.
+        dropdown = QComboBox()
+        dropdown.addItems(options)
+        if update is None:
+            dropdown.currentIndexChanged.connect(lambda index: setattr(self, name, options[index]))
+        else:
+            dropdown.currentIndexChanged.connect(update)
+
+        # Set the correct value for the value.
+        dropdown.setCurrentIndex(dropdown.findText(value))
+
+        if tooltip:
+            dropdown.setToolTip(tooltip)
+
+        layout.addWidget(dropdown)
+        return dropdown, layout
+
+    def _add_shape_param(self, names, values, min_val, max_val, step=1, title=None, tooltip=None):
+        layout = QHBoxLayout()
+
+        x_layout = QVBoxLayout()
+        x_param, _ = self._add_int_param(
+            names[0], values[0], min_val=min_val, max_val=max_val, layout=x_layout, step=step,
+            title=title[0] if title is not None else title, tooltip=tooltip
+        )
+        layout.addLayout(x_layout)
+
+        y_layout = QVBoxLayout()
+        y_param, _ = self._add_int_param(
+            names[1], values[1], min_val=min_val, max_val=max_val, layout=y_layout, step=step,
+            title=title[1] if title is not None else title, tooltip=tooltip
+        )
+        layout.addLayout(y_layout)
+
+        return x_param, y_param, layout
+
+    def _make_collapsible(self, widget, title):
+        parent_widget = QWidget()
+        parent_widget.setLayout(QVBoxLayout())
+        collapsible = QCollapsible(title, parent_widget)
+        collapsible.addWidget(widget)
+        parent_widget.layout().addWidget(collapsible)
+        return parent_widget
+    
+    def _add_boolean_param(self, name, value, title=None, tooltip=None):
+        checkbox = QCheckBox(name if title is None else title)
+        checkbox.setChecked(value)
+        checkbox.stateChanged.connect(lambda val: setattr(self, name, val))
+        if tooltip:
+            checkbox.setToolTip(tooltip)
+        return checkbox
+
+    def _add_path_param(self, name, value, select_type, title=None, placeholder=None, tooltip=None):
+        assert select_type in ("directory", "file", "both")
+
+        layout = QtWidgets.QHBoxLayout()
+        label = QtWidgets.QLabel(title or name)
+        if tooltip:
+            label.setToolTip(tooltip)
+        layout.addWidget(label)
+
+        path_textbox = QtWidgets.QLineEdit()
+        path_textbox.setText(str(value))
+        if placeholder is not None:
+            path_textbox.setPlaceholderText(placeholder)
+        path_textbox.textChanged.connect(lambda val: setattr(self, name, val))
+        if tooltip:
+            path_textbox.setToolTip(tooltip)
+
+        layout.addWidget(path_textbox)
+
+        def add_path_button(select_type, tooltip=None):
+            # Adjust button text.
+            button_text = f"Select {select_type.capitalize()}"
+            path_button = QtWidgets.QPushButton(button_text)
+
+            # Call appropriate function based on select_type.
+            path_button.clicked.connect(lambda: getattr(self, f"_get_{select_type}_path")(name, path_textbox))
+            if tooltip:
+                path_button.setToolTip(tooltip)
+            layout.addWidget(path_button)
+
+        if select_type == "both":
+            add_path_button("file")
+            add_path_button("directory")
+
+        else:
+            add_path_button(select_type)
+
+        return path_textbox, layout
+
+    def _get_directory_path(self, name, textbox, tooltip=None):
+        directory = QtWidgets.QFileDialog.getExistingDirectory(
+            self, "Select Directory", "", QtWidgets.QFileDialog.ShowDirsOnly
+        )
+        if tooltip:
+            directory.setToolTip(tooltip)
+        if directory and Path(directory).is_dir():
+            textbox.setText(str(directory))
+        else:
+            # Handle the case where the selected path is not a directory
+            print("Invalid directory selected. Please try again.")
+
+    def _get_file_path(self, name, textbox, tooltip=None):
+        file_path, _ = QtWidgets.QFileDialog.getOpenFileName(
+            self, "Select File", "", "All Files (*)"
+        )
+        if tooltip:
+            file_path.setToolTip(tooltip)
+        if file_path and Path(file_path).is_file():
+            textbox.setText(str(file_path))
+        else:
+            # Handle the case where the selected path is not a file
+            print("Invalid file selected. Please try again.")