load bad pixels from file (done)

Author: stevehenke

src/ptychodus/__main__.py

@@ -23,7 +23,7 @@ def verify_all_arguments_parsed(parser: argparse.ArgumentParser, argv: list[str]
 def main() -> int:
     parser = argparse.ArgumentParser(
         prog=ptychodus.__name__.lower(),
-        description=f'{ptychodus.__name__} is a ptychography analysis application',
+        description=f'{ptychodus.__name__} is a ptychography data analysis application',
     )
     parser.add_argument(
         '-b',

src/ptychodus/controller/patterns/core.py

@@ -2,7 +2,17 @@
 
 
 from PyQt5.QtCore import QModelIndex
-from PyQt5.QtWidgets import QAbstractItemView, QFormLayout, QMessageBox
+from PyQt5.QtWidgets import (
+    QAbstractItemView,
+    QFormLayout,
+    QHBoxLayout,
+    QLineEdit,
+    QMessageBox,
+    QPushButton,
+    QWidget,
+)
+
+from ptychodus.api.parametric import PathParameter, StringParameter
 
 from ...model.metadata import MetadataPresenter
 from ...model.patterns import (
@@ -17,16 +27,80 @@
 from ...view.widgets import ExceptionDialog, ProgressBarItemDelegate
 from ..data import FileDialogFactory
 from ..image import ImageController
-from ..parametric import LengthWidgetParameterViewController, SpinBoxParameterViewController
+from ..parametric import (
+    LengthWidgetParameterViewController,
+    ParameterViewController,
+    SpinBoxParameterViewController,
+)
 from .dataset import DatasetTreeModel
-from .dataset_file_layout import DatasetFileLayoutViewController
+from .dataset_layout import DatasetLayoutViewController
 from .wizard import OpenDatasetWizardController
 
 logger = logging.getLogger(__name__)
 
 
+class BadPixelsViewController(ParameterViewController):
+    def __init__(
+        self,
+        bad_pixels_file_path: PathParameter,
+        bad_pixels_file_type: StringParameter,
+        patterns_api: PatternsAPI,
+        file_dialog_factory: FileDialogFactory,
+    ) -> None:
+        self._bad_pixels_file_path = bad_pixels_file_path
+        self._bad_pixels_file_type = bad_pixels_file_type
+        self._patterns_api = patterns_api
+        self._file_dialog_factory = file_dialog_factory
+
+        self._line_edit = QLineEdit()
+        self._line_edit.setReadOnly(True)
+        self._browse_button = QPushButton('Browse...')
+        self._browse_button.clicked.connect(self._open_bad_pixels)
+        self._clear_button = QPushButton('Clear')
+        self._clear_button.clicked.connect(self._patterns_api.clear_bad_pixels)
+        self._widget = QWidget()
+
+        layout = QHBoxLayout()
+        layout.setContentsMargins(0, 0, 0, 0)
+        layout.addWidget(self._line_edit)
+        layout.addWidget(self._browse_button)
+        layout.addWidget(self._clear_button)
+        self._widget.setLayout(layout)
+
+        self.set_num_bad_pixels(0)
+
+    def _open_bad_pixels(self) -> None:
+        file_reader_chooser = self._patterns_api.get_bad_pixels_file_reader_chooser()
+        current_plugin = file_reader_chooser.get_current_plugin()
+        file_path, name_filter = self._file_dialog_factory.get_open_file_path(
+            self._widget,
+            'Open Bad Pixels File',
+            name_filters=[plugin.display_name for plugin in file_reader_chooser],
+            selected_name_filter=current_plugin.simple_name,
+        )
+
+        if file_path:
+            try:
+                self._patterns_api.open_bad_pixels(file_path, file_type=name_filter)
+            except Exception as exc:
+                logger.exception(exc)
+                ExceptionDialog.show_exception('Bad Pixels File Reader', exc)
+
+    def get_widget(self) -> QWidget:
+        return self._widget
+
+    def set_num_bad_pixels(self, num_bad_pixels: int) -> None:
+        self._line_edit.setText(str(num_bad_pixels))
+
+
 class DetectorController:
-    def __init__(self, settings: DetectorSettings, view: DetectorView) -> None:
+    def __init__(
+        self,
+        settings: DetectorSettings,
+        patterns_api: PatternsAPI,
+        view: DetectorView,
+        file_dialog_factory: FileDialogFactory,
+    ) -> None:
         self._width_px_view_controller = SpinBoxParameterViewController(settings.width_px)
         self._height_px_view_controller = SpinBoxParameterViewController(settings.height_px)
         self._pixel_width_view_controller = LengthWidgetParameterViewController(
@@ -36,15 +110,25 @@ def __init__(self, settings: DetectorSettings, view: DetectorView) -> None:
             settings.pixel_height_m
         )
         self._bit_depth_view_controller = SpinBoxParameterViewController(settings.bit_depth)
+        self._bad_pixels_view_controller = BadPixelsViewController(
+            settings.bad_pixels_file_path,
+            settings.bad_pixels_file_type,
+            patterns_api,
+            file_dialog_factory,
+        )
 
         layout = QFormLayout()
         layout.addRow('Detector Width [px]:', self._width_px_view_controller.get_widget())
         layout.addRow('Detector Height [px]:', self._height_px_view_controller.get_widget())
         layout.addRow('Pixel Width:', self._pixel_width_view_controller.get_widget())
         layout.addRow('Pixel Height:', self._pixel_height_view_controller.get_widget())
         layout.addRow('Bit Depth:', self._bit_depth_view_controller.get_widget())
+        layout.addRow('Bad Pixels:', self._bad_pixels_view_controller.get_widget())
         view.setLayout(layout)
 
+    def set_num_bad_pixels(self, num_bad_pixels: int) -> None:
+        self._bad_pixels_view_controller.set_num_bad_pixels(num_bad_pixels)
+
 
 class PatternsController(DiffractionDatasetObserver):
     def __init__(
@@ -66,7 +150,9 @@ def __init__(
         self._view = view
         self._image_controller = image_controller
         self._file_dialog_factory = file_dialog_factory
-        self._detector_controller = DetectorController(detector_settings, view.detector_view)
+        self._detector_controller = DetectorController(
+            detector_settings, patterns_api, view.detector_view, file_dialog_factory
+        )
         self._wizard_controller = OpenDatasetWizardController(
             pattern_settings,
             pattern_sizer,
@@ -83,17 +169,14 @@ def __init__(
         view.tree_view.selectionModel().currentChanged.connect(self._update_view)
         self._update_view(QModelIndex(), QModelIndex())
 
-        open_bad_pixels_action = view.button_box.load_menu.addAction('Open Bad Pixels...')
-        open_bad_pixels_action.triggered.connect(self._open_bad_pixels)
-
-        open_dataset_action = view.button_box.load_menu.addAction('Open Dataset...')
+        open_dataset_action = view.button_box.load_menu.addAction('Open File...')
         open_dataset_action.triggered.connect(self._wizard_controller.open_dataset)
 
         view.button_box.save_button.clicked.connect(self._save_dataset)
         view.button_box.close_button.clicked.connect(self._close_dataset)
 
-        file_layout_action = view.button_box.analyze_menu.addAction('Dataset File Layout...')
-        file_layout_action.triggered.connect(self._show_file_layout)
+        dataset_layout_action = view.button_box.analyze_menu.addAction('Dataset Layout...')
+        dataset_layout_action.triggered.connect(self._show_dataset_layout)
 
         dataset.add_observer(self)
         self._sync_model_to_view()
@@ -107,23 +190,6 @@ def _update_view(self, current: QModelIndex, previous: QModelIndex) -> None:
         else:
             self._image_controller.clear_array()
 
-    def _open_bad_pixels(self) -> None:
-        file_reader_chooser = self._patterns_api.get_bad_pixels_file_reader_chooser()
-        current_plugin = file_reader_chooser.get_current_plugin()
-        file_path, name_filter = self._file_dialog_factory.get_open_file_path(
-            self._view,
-            'Open Bad Pixels File',
-            name_filters=[plugin.simple_name for plugin in file_reader_chooser],
-            selected_name_filter=current_plugin.simple_name,
-        )
-
-        if file_path:
-            try:
-                self._patterns_api.load_bad_pixels(file_path, file_type=name_filter)
-            except Exception as exc:
-                logger.exception(exc)
-                ExceptionDialog.show_exception('Bad Pixels File Reader', exc)
-
     def _save_dataset(self) -> None:
         file_writer_chooser = self._patterns_api.get_file_writer_chooser()
         file_path, name_filter = self._file_dialog_factory.get_save_file_path(
@@ -140,8 +206,8 @@ def _save_dataset(self) -> None:
                 logger.exception(exc)
                 ExceptionDialog.show_exception('File Writer', exc)
 
-    def _show_file_layout(self) -> None:
-        DatasetFileLayoutViewController.show_dialog(self._dataset, self._view)
+    def _show_dataset_layout(self) -> None:
+        DatasetLayoutViewController.show_dialog(self._dataset, self._view)
 
     def _close_dataset(self) -> None:
         button = QMessageBox.question(
@@ -162,6 +228,9 @@ def _sync_model_to_view(self) -> None:
         info_text = self._dataset.get_info_text()
         self._view.info_label.setText(info_text)
 
+    def handle_bad_pixels_changed(self, num_bad_pixels: int) -> None:
+        self._detector_controller.set_num_bad_pixels(num_bad_pixels)
+
     def handle_array_inserted(self, index: int) -> None:
         self._tree_model.insert_array(index, self._dataset[index])
 

…ntroller/patterns/dataset_file_layout.py …us/controller/patterns/dataset_layout.pysrc/ptychodus/controller/patterns/dataset_file_layout.py renamed to src/ptychodus/controller/patterns/dataset_layout.py src/ptychodus/controller/patterns/dataset_file_layout.py renamed to src/ptychodus/controller/patterns/dataset_layout.py

@@ -91,7 +91,7 @@ def columnCount(self, parent: QModelIndex = QModelIndex()) -> int:  # noqa: N802
         return len(node.item_data)
 
 
-class DatasetFileLayoutViewController(DiffractionDatasetObserver):
+class DatasetLayoutViewController(DiffractionDatasetObserver):
     def __init__(self, dataset: AssembledDiffractionDataset, tree_model: SimpleTreeModel) -> None:
         super().__init__()
         self._dataset = dataset
@@ -113,6 +113,9 @@ def show_dialog(cls, dataset: AssembledDiffractionDataset, parent: QWidget) -> N
     def _sync_model_to_view(self) -> None:
         self._tree_model.set_root_node(self._dataset.get_contents_tree())
 
+    def handle_bad_pixels_changed(self, num_bad_pixels: int) -> None:
+        pass
+
     def handle_array_inserted(self, index: int) -> None:
         pass
 

src/ptychodus/model/metadata.py

@@ -127,6 +127,9 @@ def sync_detector_distance(self) -> None:
         if distance_m:
             self._product_settings.detector_distance_m.set_value(distance_m)
 
+    def handle_bad_pixels_changed(self, num_bad_pixels: int) -> None:
+        pass
+
     def handle_array_inserted(self, index: int) -> None:
         pass
 

src/ptychodus/model/patterns/api.py

@@ -67,7 +67,7 @@ def create_streaming_context(self, metadata: DiffractionMetadata) -> PatternsStr
     def get_bad_pixels_file_reader_chooser(self) -> PluginChooser[BadPixelsFileReader]:
         return self._bad_pixels_file_reader_chooser
 
-    def load_bad_pixels(self, file_path: Path, *, file_type: str | None = None) -> None:
+    def open_bad_pixels(self, file_path: Path, *, file_type: str | None = None) -> None:
         if file_path.is_file():
             if file_type is not None:
                 self._bad_pixels_file_reader_chooser.set_current_plugin(file_type)
@@ -84,6 +84,9 @@ def load_bad_pixels(self, file_path: Path, *, file_type: str | None = None) -> N
         else:
             logger.warning(f'Refusing to read invalid file path {file_path}')
 
+    def clear_bad_pixels(self) -> None:
+        self._dataset.set_bad_pixels(None)
+
     def get_file_reader_chooser(self) -> PluginChooser[DiffractionFileReader]:
         return self._file_reader_chooser
 

src/ptychodus/model/patterns/core.py

@@ -57,7 +57,7 @@ def stop(self) -> None:
 
     def _update(self, observable: Observable) -> None:
         if observable is self._reinit_observable:
-            self.patterns_api.load_bad_pixels(
+            self.patterns_api.open_bad_pixels(
                 file_path=self.detector_settings.bad_pixels_file_path.get_value(),
                 file_type=self.detector_settings.bad_pixels_file_type.get_value(),
             )

src/ptychodus/model/patterns/dataset.py

@@ -38,6 +38,10 @@
 
 
 class DiffractionDatasetObserver(ABC):
+    @abstractmethod
+    def handle_bad_pixels_changed(self, num_bad_pixels: int) -> None:
+        pass
+
     @abstractmethod
     def handle_array_inserted(self, index: int) -> None:
         pass
@@ -275,8 +279,25 @@ def get_metadata(self) -> DiffractionMetadata:
         return self._metadata
 
     def set_bad_pixels(self, bad_pixels: BadPixelsArray | None) -> None:
+        if bad_pixels is not None:
+            if bad_pixels.ndim != 2:
+                raise ValueError(f'Bad pixels array must be 2D, got {bad_pixels.ndim}D.')
+
+            actual_extent = ImageExtent(
+                width_px=bad_pixels.shape[-1], height_px=bad_pixels.shape[-2]
+            )
+            expected_extent = self._sizer.get_detector_extent()
+
+            if actual_extent != expected_extent:
+                raise ValueError(f'Shape mismatch: {actual_extent=} {expected_extent=}')
+
         self._bad_pixels = bad_pixels
 
+        num_bad_pixels = 0 if self._bad_pixels is None else numpy.count_nonzero(self._bad_pixels)
+
+        for observer in self._observer_list:
+            observer.handle_bad_pixels_changed(num_bad_pixels)
+
     def get_bad_pixels(self) -> BadPixelsArray | None:
         return self._bad_pixels
 

src/ptychodus/model/patterns/processor.py

@@ -88,7 +88,6 @@ class DiffractionPatternProcessor:
     transpose: bool
 
     def process_bad_pixels(self, bad_pixels: BadPixelsArray) -> BadPixelsArray:
-        # FIXME sync bad pixels file_path to settings in controller?
         if bad_pixels.ndim != 2:
             raise ValueError(f'Invalid bad_pixel dimensions! (shape={bad_pixels.shape})')