Merge pull request #28 from TimMonko/utilities-container

Add Utilities Container Widget

src/napari_ndev/__init__.py

@@ -4,6 +4,7 @@
     __version__ = "unknown"
 
 from ._napari_utilities import annotation_saver, rescale_by
+from ._utilities_container import MetaImg
 from ._widget import (
     batch_predict,
     batch_training,
@@ -18,4 +19,5 @@
     "batch_predict",
     "batch_training",
     "rescale_by",
+    "MetaImg",
 ]

src/napari_ndev/_utilities_container.py

@@ -0,0 +1,276 @@
+import ast
+import os
+from pathlib import Path
+from typing import TYPE_CHECKING, List, Union
+
+import dask.array as da
+import numpy as np
+import xarray as xr
+from aicsimageio import AICSImage
+from aicsimageio.types import PhysicalPixelSizes
+from aicsimageio.writers import OmeTiffWriter
+from magicgui.widgets import (
+    CheckBox,
+    Container,
+    FileEdit,
+    FloatSpinBox,
+    PushButton,
+    Select,
+    TextEdit,
+    create_widget,
+)
+from napari import layers
+from napari.viewer import current_viewer
+
+if TYPE_CHECKING:
+    import napari
+
+PathLike = Union[str, Path]
+ArrayLike = Union[np.ndarray, da.Array]
+MetaArrayLike = Union[ArrayLike, xr.DataArray]
+ImageLike = Union[
+    PathLike, ArrayLike, MetaArrayLike, List[MetaArrayLike], List[PathLike]
+]
+
+
+class MetaImg(Container):
+    def __init__(
+        self,
+        viewer: "napari.viewer.Viewer",
+    ):
+        super().__init__()
+        self
+        self._viewer = viewer
+        self._img_data = None
+        self._layer_save_dims = None
+        self._p_sizes = None
+
+        self._files = FileEdit(label="File(s)", mode="rm")
+
+        self._open_image_button = PushButton(label="Open Images")
+
+        self._save_directory = FileEdit(label="Save Directory", mode="d")
+        self._save_name = create_widget(
+            annotation=str, value=None, label="File Save Name"
+        )
+
+        self._metadata_from_selected_layer = PushButton(
+            label="Update Metadata from Selected Layer"
+        )
+
+        self._dim_order = create_widget(
+            annotation=str, label="Dimension Order"
+        )
+        self._channel_names = create_widget(
+            annotation=str, label="Channel Name(s)"
+        )
+
+        self._physical_pixel_sizes_z = FloatSpinBox(
+            value=1, step=0.00000001, label="Z Pixel Size, um"
+        )
+        self._physical_pixel_sizes_y = FloatSpinBox(
+            value=1, step=0.00000001, label="Y Pixel Size, um"
+        )
+        self._physical_pixel_sizes_x = FloatSpinBox(
+            value=1, step=0.00000001, label="X Pixel Size, um"
+        )
+
+        def current_layers(_):
+            return [
+                x
+                for x in current_viewer().layers
+                if isinstance(x, layers.Image)
+            ]
+
+        self._image_layer = Select(
+            choices=current_layers, nullable=False, label="Images"
+        )  # use no value and allow user to unhighlight layers
+
+        self._concatenate_image_files = CheckBox(label="Concatenate Files")
+        self._concatenate_image_layers = CheckBox(
+            label="Concatenate Image Layers"
+        )
+
+        self._save_image_button = PushButton(label="Save Images")
+
+        self._labels_layer = create_widget(
+            annotation="napari.layers.Labels", label="Labels"
+        )
+        self._save_labels_button = PushButton(label="Save Labels")
+
+        self._shapes_layer = create_widget(
+            annotation="napari.layers.Shapes", label="Shapes"
+        )
+        self._save_shapes_button = PushButton(label="Save Shapes as Labels")
+
+        self._results = TextEdit(label="Info")
+
+        # Container Widget Order
+        self.extend(
+            [
+                self._files,
+                self._open_image_button,
+                self._dim_order,
+                self._channel_names,
+                self._physical_pixel_sizes_z,
+                self._physical_pixel_sizes_y,
+                self._physical_pixel_sizes_x,
+                self._image_layer,
+                self._metadata_from_selected_layer,
+                self._concatenate_image_files,
+                self._concatenate_image_layers,
+                self._save_directory,
+                self._save_name,
+                self._save_image_button,
+                self._labels_layer,
+                self._save_labels_button,
+                self._shapes_layer,
+                self._save_shapes_button,
+                self._results,
+            ]
+        )
+
+        # Callbacks
+        self._files.changed.connect(self.update_metadata_from_file)
+        self._open_image_button.clicked.connect(self.open_images)
+        self._metadata_from_selected_layer.clicked.connect(
+            self.update_metadata_from_layer
+        )
+
+        self._save_image_button.clicked.connect(self.save_ome_tiff)
+        self._save_labels_button.clicked.connect(self.save_labels)
+        self._save_shapes_button.clicked.connect(self.save_shapes_as_labels)
+        self._results._on_value_change()
+
+    def _update_metadata(self, img):
+        self._dim_order.value = img.dims.order
+        self._layer_save_dims = "".join(
+            [
+                d
+                for d in img.dims.order
+                if d != "C" and img.dims._dims_shape[d] > 1
+            ]
+        )
+        self._channel_names.value = img.channel_names
+
+        if img.physical_pixel_sizes.Z is not None:
+            self._physical_pixel_sizes_z.value = img.physical_pixel_sizes.Z
+        elif img.physical_pixel_sizes.Z is None:
+            self._physical_pixel_sizes_z.value = 0
+        self._physical_pixel_sizes_y.value = img.physical_pixel_sizes.Y
+        self._physical_pixel_sizes_x.value = img.physical_pixel_sizes.X
+
+        self._save_name.value = str(
+            os.path.splitext(os.path.basename(self._files.value[0]))[0]
+            + ".tif"
+        )
+
+    def update_metadata_from_file(self):
+        print(self._files.value[0])
+        img = AICSImage(self._files.value[0])
+        self._img = img
+        self._update_metadata(img)
+
+    def update_metadata_from_layer(self):
+        img = self._image_layer.value[0].metadata["aicsimage"]
+        self._img = img
+        self._update_metadata(img)
+
+    def open_images(self):
+        self._viewer.open(self._files.value, plugin="napari-aicsimageio")
+
+    def concatenate_images(self):
+        array_list = []
+        if self._concatenate_image_files.value:
+            for file in self._files.value:
+                img = AICSImage(file)
+
+                for idx, _ in enumerate(img.channel_names):
+                    array = img.data[:, [idx], :, :, :]
+
+                    if array.max() > 0:
+                        array_list.append(array)
+
+        if self._concatenate_image_layers.value:
+            for layer in self._image_layer.value:
+                print(layer.data.shape)
+                layer_reshape = layer.data[np.newaxis, np.newaxis, np.newaxis]
+                array_list.append(layer_reshape)
+
+        self._img_data = np.concatenate(array_list, axis=1)
+
+    def _get_p_sizes(self):
+        self._p_sizes = PhysicalPixelSizes(
+            self._physical_pixel_sizes_z.value,
+            self._physical_pixel_sizes_y.value,
+            self._physical_pixel_sizes_x.value,
+        )
+
+    def _get_save_loc(self, parent):
+        save_directory = self._save_directory.value / parent
+        save_directory.mkdir(parents=False, exist_ok=True)
+        save_loc = save_directory / self._save_name.value
+        return save_loc
+
+    def save_ome_tiff(self):
+        self.concatenate_images()
+        self._get_p_sizes()
+        img_save_loc = self._get_save_loc("Images")
+
+        try:
+            OmeTiffWriter.save(
+                data=self._img_data,
+                uri=img_save_loc,
+                dim_order=self._dim_order.value,
+                channel_names=ast.literal_eval(self._channel_names.value),
+                physical_pixel_sizes=self._p_sizes,
+            )
+            # print("saved:", self._save_name.value)
+            self._results.value = "Saved image: " + str(self._save_name.value)
+
+        except ValueError as e:
+            OmeTiffWriter.save(
+                data=self._img_data,
+                uri=img_save_loc,
+                dim_order=self._dim_order.value,
+                physical_pixel_sizes=self._p_sizes,
+            )
+            self._results.value = (
+                "ValueError: "
+                + str(e)
+                + "\nSo, saved with default file names: \n"
+                + str(self._save_name.value)
+            )
+
+    def save_labels(self):
+        lbl = self._labels_layer.value.data
+        self._get_p_sizes()
+        lbl_save_loc = self._get_save_loc("Labels")
+
+        OmeTiffWriter.save(
+            data=lbl,
+            uri=lbl_save_loc,
+            dim_order=self._layer_save_dims,
+            channel_names=["Labels"],
+            physical_pixel_sizes=self._p_sizes,
+        )
+        self._results.value = "Saved labels: " + str(self._save_name.value)
+
+    def save_shapes_as_labels(self):
+        shapes = self._shapes_layer.value
+        label_dim = self._image_layer.value.data.shape
+        shapes_as_labels = shapes.to_labels(labels_shape=label_dim)
+
+        self._get_p_sizes()
+        shapes_save_loc = self._get_save_loc("Shapes")
+
+        OmeTiffWriter.save(
+            data=shapes_as_labels,
+            uri=shapes_save_loc,
+            dim_order=self._layer_save_dims,
+            channel_names=["Shapes"],
+            physical_pixel_sizes=self._p_sizes,
+        )
+        self._results.value = "Saved shapes as labels: " + str(
+            self._save_name.value
+        )

src/napari_ndev/napari.yaml

@@ -20,6 +20,9 @@ contributions:
     - id: napari-ndev.make_rescale_by
       python_name: napari_ndev._napari_utilities:rescale_by
       title: Make Rescale By Widget
+    - id: napari-ndev.make_utilities_container
+      python_name: napari_ndev._utilities_container:MetaImg
+      title: Image Utilities
 
   widgets:
     - command: napari-ndev.make_batch_utilities
@@ -34,3 +37,5 @@ contributions:
       display_name: Batch APOC Predict
     - command: napari-ndev.make_rescale_by
       display_name: Rescale By
+    - command: napari-ndev.make_utilities_container
+      display_name: Image Utilities