v0.6.0

CHANGELOG.md

@@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.6.0] - 2021-10-18
+
+Replaced imctools by readimc
+
 ## [v0.5.6] - 2021-10-05
 
 Fixed napari-imc for napari>0.4.10
@@ -24,6 +28,7 @@ Updated documentation
 Last release before introducing this changelog
 
 
+[v0.6.0]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.6...v0.6.0
 [v0.5.6]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.4...v0.5.6
 [v0.5.4]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.3...v0.5.4
 [v0.5.3]: https://github.com/BodenmillerGroup/napari-imc/compare/v0.5.1...v0.5.3

napari_imc/io/mcd.py

@@ -1,9 +1,8 @@
 import numpy as np
 
-from imageio import imread
-from imctools.io.mcd.mcdparser import McdParser
 from napari_imc.io.base import FileReaderBase, ImageDimensions
 from pathlib import Path
+from readimc import IMCMcdFile
 from typing import List, Optional, Tuple, Union
 
 from napari_imc.models import IMCFileModel, IMCFileAcquisitionModel, IMCFilePanoramaModel
@@ -12,52 +11,65 @@
 class McdFileReader(FileReaderBase):
     def __init__(self, path: Union[str, Path]):
         super(McdFileReader, self).__init__(path)
-        self._mcd_parser: Optional[McdParser] = None
+        self._mcd_file: Optional[IMCMcdFile] = None
 
     def _get_imc_file_panoramas(self, imc_file: IMCFileModel) -> List[IMCFilePanoramaModel]:
         return [
-            IMCFilePanoramaModel(imc_file, panorama.id, panorama.image_type, panorama.description)
-            for panorama in self._mcd_parser.session.panoramas.values() if panorama.image_type != 'Default'
+            IMCFilePanoramaModel(imc_file, panorama.id, panorama.metadata.get("Type"), panorama.description)
+            for slide in self._mcd_file.slides for panorama in slide.panoramas
         ]
 
     def _get_imc_file_acquisitions(self, imc_file: IMCFileModel) -> List[IMCFileAcquisitionModel]:
         return [
             IMCFileAcquisitionModel(imc_file, acquisition.id, acquisition.description, acquisition.channel_labels)
-            for acquisition in self._mcd_parser.session.acquisitions.values() if acquisition.is_valid
+            for slide in self._mcd_file.slides for acquisition in slide.acquisitions
         ]
 
     def read_panorama(self, panorama_id: int) -> Tuple[ImageDimensions, np.ndarray]:
-        panorama = self._mcd_parser.session.panoramas[panorama_id]
-        xs_physical = [panorama.x1, panorama.x2, panorama.x3, panorama.x4]
-        ys_physical = [panorama.y1, panorama.y2, panorama.y3, panorama.y4]
+        panorama = next(
+            panorama
+            for slide in self._mcd_file.slides
+            for panorama in slide.panoramas
+            if panorama.id == panorama_id
+        )
+        xs_physical = [panorama.x1_um, panorama.x2_um, panorama.x3_um, panorama.x4_um]
+        ys_physical = [panorama.y1_um, panorama.y2_um, panorama.y3_um, panorama.y4_um]
         x_physical, y_physical = min(xs_physical), min(ys_physical)
         w_physical, h_physical = max(xs_physical) - x_physical, max(ys_physical) - y_physical
-        data = imread(self._mcd_parser.get_panorama_image(panorama_id))
-        if x_physical != panorama.x1:
+        data = self._mcd_file.read_panorama(panorama)
+        if x_physical != panorama.x1_um:
             data = data[:, ::-1, :]
-        if y_physical != panorama.y1:
+        if y_physical != panorama.y1_um:
             data = data[::-1, :, :]
         return (x_physical, y_physical, w_physical, h_physical), data
 
     def read_acquisition(self, acquisition_id: int, channel_label: str) -> Tuple[ImageDimensions, np.ndarray]:
-        acquisition = self._mcd_parser.session.acquisitions[acquisition_id]
-        xs_physical = [acquisition.roi_start_x_pos_um, acquisition.roi_end_x_pos_um]
-        ys_physical = [acquisition.roi_start_y_pos_um, acquisition.roi_end_y_pos_um]
+        acquisition = next(
+            acquisition
+            for slide in self._mcd_file.slides
+            for acquisition in slide.acquisitions
+            if acquisition.id == acquisition_id
+        )
+        channel_index = acquisition.channel_labels.index(channel_label)
+        xs_physical = [acquisition.start_x_um, acquisition.end_x_um]
+        ys_physical = [acquisition.start_y_um, acquisition.end_y_um]
         x_physical, y_physical = min(xs_physical), min(ys_physical)
         w_physical, h_physical = max(xs_physical) - x_physical, max(ys_physical) - y_physical
-        data = self._mcd_parser.get_acquisition_data(acquisition.id).get_image_by_label(channel_label)
-        if x_physical != acquisition.roi_start_x_pos_um:
-            data = data[:, ::-1]
-        if y_physical != acquisition.roi_start_y_pos_um:
-            data = data[::-1, :]
-        return (x_physical, y_physical, w_physical, h_physical), data
+        channel_img = self._mcd_file.read_acquisition(acquisition)[channel_index]
+        if x_physical != acquisition.start_x_um:
+            channel_img = channel_img[:, ::-1]
+        if y_physical != acquisition.start_y_um:
+            channel_img = channel_img[::-1, :]
+        return (x_physical, y_physical, w_physical, h_physical), channel_img
 
     def __enter__(self) -> 'FileReaderBase':
-        self._mcd_parser = McdParser(self._path)
+        self._mcd_file = IMCMcdFile(self._path)
+        self._mcd_file.open()
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
-        self._mcd_parser.close()
+        self._mcd_file.close()
+        self._mcd_file = None
 
     @classmethod
     def accepts(cls, path: Union[str, Path]) -> bool:

napari_imc/io/txt.py

@@ -1,8 +1,9 @@
 import numpy as np
+import re
 
-from imctools.io.txt.txtparser import TxtParser
 from napari_imc.io.base import FileReaderBase, ImageDimensions
 from pathlib import Path
+from readimc import IMCTxtFile
 from typing import List, Optional, Tuple, Union
 
 from napari_imc.models import IMCFileModel, IMCFileAcquisitionModel, IMCFilePanoramaModel
@@ -11,34 +12,37 @@
 class TxtFileReader(FileReaderBase):
     def __init__(self, path: Union[str, Path]):
         super(TxtFileReader, self).__init__(path)
-        self._txt_parser: Optional[TxtParser] = None
+        self._txt_file: Optional[IMCTxtFile] = None
 
     def _get_imc_file_panoramas(self, imc_file: IMCFileModel) -> List[IMCFilePanoramaModel]:
         return []
 
     def _get_imc_file_acquisitions(self, imc_file: IMCFileModel) -> List[IMCFileAcquisitionModel]:
-        acquisition = self._txt_parser.get_acquisition_data().acquisition
+        m = re.match(r"(?P<description>.*)_(?P<id>[0-9]+)", self._path.stem)
+        acquisition_id = int(m.group("id")) if m is not None else 0
+        acquisition_description = m.group("description") if m is not None else self._path.stem
         return [
-            IMCFileAcquisitionModel(imc_file, acquisition.id, acquisition.description, acquisition.channel_labels)
+            IMCFileAcquisitionModel(imc_file, acquisition_id, acquisition_description, self._txt_file.channel_labels)
         ]
 
     def read_panorama(self, panorama_id: int) -> Tuple[ImageDimensions, np.ndarray]:
         raise RuntimeError('This operation is not supported')
 
     def read_acquisition(self, acquisition_id: int, channel_label: str) -> Tuple[ImageDimensions, np.ndarray]:
-        acquisition_data = self._txt_parser.get_acquisition_data()
-        acquisition = acquisition_data.acquisition
+        channel_index = self._txt_file.channel_labels.index(channel_label)
+        channel_img = self._txt_file.read_acquisition()[channel_index]
         x_physical, y_physical = 0, 0
-        w_physical, h_physical = acquisition.max_x, acquisition.max_y
-        data = acquisition_data.get_image_by_label(channel_label)
-        return (x_physical, y_physical, w_physical, h_physical), data
+        h_physical, w_physical = channel_img.shape
+        return (x_physical, y_physical, w_physical, h_physical), channel_img
 
     def __enter__(self) -> 'FileReaderBase':
-        self._txt_parser = TxtParser(self._path)
+        self._txt_file = IMCTxtFile(self._path)
+        self._txt_file.open()
         return self
 
     def __exit__(self, exc_type, exc_val, exc_tb):
-        pass
+        self._txt_file.close()
+        self._txt_file = None
 
     @classmethod
     def accepts(cls, path: Union[str, Path]) -> bool:

napari_imc/models/imc_file_panorama.py

@@ -10,7 +10,7 @@
 class IMCFilePanoramaModel(ModelBase, IMCFileTreeItem):
     imc_file_tree_is_checkable = True
 
-    def __init__(self, imc_file: 'IMCFileModel', id_: int, image_type: str,
+    def __init__(self, imc_file: 'IMCFileModel', id_: int, image_type: Optional[str],
                  description: str):
         ModelBase.__init__(self)
         IMCFileTreeItem.__init__(self)

setup.cfg

@@ -31,18 +31,19 @@ packages = find:
 python_requires = >=3.7
 setup_requires = setuptools_scm
 install_requires =
-    imageio
-    imctools
     napari
     napari-plugin-engine>=0.1.4
     numpy
     qtpy
+    readimc
     superqt
 use_scm_version =
     write_to = napari_czifile2/version.py
 
 [options.extras_require]
-IMAXT = zarr
+IMAXT =
+    imageio
+    zarr
 
 [options.entry_points]
 napari.plugin =