code formatting

src/depiction/calibration/perform_calibration.py

@@ -46,7 +46,7 @@ def __init__(
     #        raise ValueError(f"Unknown pattern={repr(pattern)}")
 
     def _validate_per_spectra_array(self, array: DataArray, coordinates_2d) -> None:
-        """Checks the DataArray has the correct shapes and dimensions. Used for debugging. """
+        """Checks the DataArray has the correct shapes and dimensions. Used for debugging."""
         # TODO make it configurable in the future, whether this check is executed, during development it definitely
         #      should be here since it can safe a ton of time
         expected_coords = {"i", "x", "y"}
@@ -102,8 +102,9 @@ def _extract_all_features(self, read_peaks: ImzmlReadFile) -> DataArray:
             ),
             reduce_fn=lambda chunks: xarray.concat(chunks, dim="i"),
         )
-        return all_features.assign_coords(x=("i", read_peaks.coordinates_2d[:, 0]),
-                                          y=("i", read_peaks.coordinates_2d[:, 1]))
+        return all_features.assign_coords(
+            x=("i", read_peaks.coordinates_2d[:, 0]), y=("i", read_peaks.coordinates_2d[:, 1])
+        )
 
     def _apply_all_models(
         self, read_file: ImzmlReadFile, write_file: ImzmlWriteFile, all_model_coefs: DataArray

src/depiction/calibration/spectrum/calibration_pipeline_chemical_peptide_noise.py

@@ -41,7 +41,8 @@ def fit_spectrum_model(self, features: DataArray) -> DataArray:
         #    us to provide the information about mz_arr, which also risks breaking the abstraction again
         return features
 
-    def apply_spectrum_model(self, spectrum_mz_arr: NDArray[float], spectrum_int_arr: NDArray[float],
-                             model_coef: DataArray) -> tuple[NDArray[float], NDArray[float]]:
+    def apply_spectrum_model(
+        self, spectrum_mz_arr: NDArray[float], spectrum_int_arr: NDArray[float], model_coef: DataArray
+    ) -> tuple[NDArray[float], NDArray[float]]:
         res_mz_arr = self._calibration.align_masses(mz_arr=spectrum_mz_arr, int_arr=spectrum_int_arr)
         return res_mz_arr, spectrum_int_arr

src/depiction/evaluate_normalization.py

@@ -2,6 +2,7 @@
 
 # TODO deprecated, use tools.normalize_intensities instead
 
+
 class EvaluateTICNormalization:
     """
     Evaluates the TIC normalization of spectra.

src/depiction/image/sparse_image_2d.py

@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 # file is deprecated, use MultiChannelImage instead!
 
 import warnings

src/depiction/misc/experimental/dash_data_visualizer_exp1.py

@@ -99,7 +99,6 @@ def display_altair_chart(active_cell):
         .add_params(brush)
     )
 
-
     plot_hist = (
         alt.Chart(channel_df)
         .mark_bar()

src/depiction/misc/experimental/dash_data_visualizer_exp2.py

@@ -50,13 +50,13 @@ def better_from_dense(x):
     [
         html.H3("Select a marker of interest"),
         dcc.Dropdown(df["Marker"].tolist(), id="marker-dropdown", value=df["Marker"].iloc[0], clearable=False),
-        #dash_table.DataTable(
+        # dash_table.DataTable(
         #    id="table",
         #    columns=[{"name": i, "id": i} for i in df.columns],
         #    data=df.to_dict("records"),
         #    style_table={"height": "300px", "overflowY": "auto"},
         #    active_cell={"row": 0, "column": 0},
-        #),
+        # ),
         html.H3("Visualization"),
         dvc.Vega(id="altair-chart", opt={"actions": False}),
     ],
@@ -70,12 +70,12 @@ def better_from_dense(x):
 ########    return [{"if": {"row_index": active_cell["row"]}, "backgroundColor": "#3D9970"}]
 
 
-#@callback(Output("altair-chart", "spec"), Input("table", "active_cell"))
-#def display_altair_chart(active_cell):
-@callback(Output("altair-chart","spec"), Input("marker-dropdown","value"))
+# @callback(Output("altair-chart", "spec"), Input("table", "active_cell"))
+# def display_altair_chart(active_cell):
+@callback(Output("altair-chart", "spec"), Input("marker-dropdown", "value"))
 def display_altair_chart(marker_name):
-    #i_channel = active_cell["row"]
-    i_channel = df[df["Marker"]==marker_name].index[0]
+    # i_channel = active_cell["row"]
+    i_channel = df[df["Marker"] == marker_name].index[0]
     coordinates_2d = ion_images.sparse_coordinates
     channel_df = pd.DataFrame(
         {
@@ -103,7 +103,6 @@ def display_altair_chart(marker_name):
         .add_params(brush)
     )
 
-
     plot_hist = (
         alt.Chart(channel_df)
         .mark_bar()

src/depiction/misc/experimental/prototype_scan_registration.py

@@ -125,7 +125,7 @@ def get_sd_img_channels(channel_img_path: Path, area_coords: NDArray) -> spatial
     # fill nan (TODO)
     flipped_img = flipped_img.copy()
     # TODO?
-    #flipped_img = flipped_img.fillna(-1.0)
+    # flipped_img = flipped_img.fillna(-1.0)
     # normalize (TODO reconsider)
     # flipped_img = ImageNormalization().normalize_xarray(flipped_img, ImageNormalizationVariant.VEC_NORM)
     return spatialdata.models.Image2DModel.parse(

src/depiction/misc/experimental/synthetic_maldi_ihc_data.py

@@ -47,7 +47,7 @@ def generate_label_image_circles(
                         label_image[h, w, i_label] = 1
 
         data = DataArray(label_image, dims=("y", "x", "c"), coords={"c": [f"synthetic_{i}" for i in range(n_labels)]})
-        data["bg_value"] = 0.
+        data["bg_value"] = 0.0
         return MultiChannelImage(data)
 
     def generate_imzml_for_labels(

src/depiction/parallel_ops/parallel_map.py

@@ -9,6 +9,7 @@
 
 if TYPE_CHECKING:
     from depiction.parallel_ops import ParallelConfig
+
     S = TypeVar("S")
     T = TypeVar("T")
     U = TypeVar("U")

src/depiction/parallel_ops/read_spectra_parallel.py

@@ -14,6 +14,7 @@
 if TYPE_CHECKING:
     from numpy.typing import NDArray
     from depiction.persistence import ImzmlReadFile, ImzmlReader
+
     T = TypeVar("T")
     V = TypeVar("V")
 

src/depiction/persistence/imzml_reader.py

@@ -56,7 +56,7 @@ def __getstate__(self) -> dict[str, Any]:
             "int_arr_dtype": self._int_arr_dtype,
             "mz_bytes": self._mz_bytes,
             "int_bytes": self._int_bytes,
-            "coordinates": self._coordinates
+            "coordinates": self._coordinates,
         }
 
     # TODO
@@ -215,5 +215,7 @@ def parse_imzml(cls, path: Path) -> ImzmlReader:
         )
 
     def __str__(self) -> str:
-        return (f"ImzmlReader[{self._imzml_path}, n_spectra={self.n_spectra},"
-                f" int_arr_dtype={self._int_arr_dtype}, mz_arr_dtype={self._mz_arr_dtype}]")
+        return (
+            f"ImzmlReader[{self._imzml_path}, n_spectra={self.n_spectra},"
+            f" int_arr_dtype={self._int_arr_dtype}, mz_arr_dtype={self._mz_arr_dtype}]"
+        )

src/depiction/persistence/imzml_writer.py

@@ -19,7 +19,7 @@ def __init__(
         self,
         *,
         wrapped_imzml_writer: pyimzml.ImzMLWriter.ImzMLWriter,
-        imzml_alignment_tracker: Optional[ImzmlAlignmentTracker]
+        imzml_alignment_tracker: Optional[ImzmlAlignmentTracker],
     ) -> None:
         self._imzml_writer = wrapped_imzml_writer
         self._imzml_alignment_tracker = imzml_alignment_tracker
@@ -70,7 +70,7 @@ def add_spectrum(
     ) -> None:
         if len(mz_arr) != len(int_arr):
             raise ValueError(f"{len(mz_arr)=} and {len(int_arr)=} must be equal.")
-        
+
         # Handle alignment check information.
         if self._imzml_alignment_tracker:
             self._imzml_alignment_tracker.track_mz_array(mz_arr)
@@ -96,9 +96,12 @@ def copy_spectra(
         :param spectra_indices: The indices of the spectra to copy.
         """
         if tqdm_position is not None:
+
             def progress_fn(x):
                 return tqdm(x, desc=" spectrum", position=tqdm_position)
+
         else:
+
             def progress_fn(x):
                 return x
 

src/depiction/persistence/pixel_size.py

@@ -6,4 +6,3 @@ class PixelSize:
     size_x: float
     size_y: float
     unit: str
-

src/depiction/persistence/ram_write_file.py

@@ -22,13 +22,13 @@ def __init__(self, imzml_mode: ImzmlModeEnum) -> None:
     def imzml_mode(self):
         return self._imzml_mode
 
-    #Just for the sake of a clean api this does not really belong here...
-    #def add_spectrum(
+    # Just for the sake of a clean api this does not really belong here...
+    # def add_spectrum(
     #    self,
     #    mz_arr: np.ndarray,
     #    int_arr: np.ndarray,
     #    coordinates: tuple[int, int] | tuple[int, int, int],
-    #):
+    # ):
     #    self._mz_arr.append(mz_arr)
     #    self._int_arr.append(int_arr)
     #    self._coordinates.append(coordinates)
@@ -58,9 +58,12 @@ def add_spectrum(self, mz_arr: np.ndarray, int_arr: np.ndarray, coordinates) ->
     def copy_spectra(self, reader, spectra_indices: Sequence[int], tqdm_position: int | None = None) -> None:
         # TODO reuse the implementation from ImzmlWriter as this is 100% identical
         if tqdm_position is not None:
+
             def progress_fn(x):
                 return tqdm(x, desc=" spectrum", position=tqdm_position)
+
         else:
+
             def progress_fn(x):
                 return x
 

src/depiction/spectrum/baseline/baseline.py

@@ -8,7 +8,7 @@ class Baseline(Protocol):
     """Baseline estimation and subtraction protocol."""
 
     def evaluate_baseline(self, mz_arr: NDArray[float], int_arr: NDArray[float]) -> NDArray[float]:
-        """Returns the spectrum intensities of the baseline. """
+        """Returns the spectrum intensities of the baseline."""
         raise NotImplementedError()
 
     def subtract_baseline(self, mz_arr: NDArray[float], int_arr: NDArray[float]) -> NDArray[float]:

src/depiction/spectrum/evaluate_bins.py

@@ -46,7 +46,9 @@ def evaluate(self, mz_arr: NDArray[float], int_arr: NDArray[float]) -> NDArray[f
             self._statistic.value,
         )
 
-    def evaluate_file(self, read_file: ImzmlReadFile, write_file: ImzmlWriteFile, parallel_config: ParallelConfig) -> None:
+    def evaluate_file(
+        self, read_file: ImzmlReadFile, write_file: ImzmlWriteFile, parallel_config: ParallelConfig
+    ) -> None:
         write_parallel = WriteSpectraParallel.from_config(parallel_config)
         write_parallel.map_chunked_to_file(
             read_file=read_file,

src/depiction/spectrum/peak_picking/__init__.py

@@ -1,7 +1,4 @@
 from .basic_peak_picker import BasicPeakPicker
 from .basic_interpolated_peak_picker import BasicInterpolatedPeakPicker
 
-__all__ = [
-    "BasicPeakPicker",
-    "BasicInterpolatedPeakPicker"
-]
+__all__ = ["BasicPeakPicker", "BasicInterpolatedPeakPicker"]

src/depiction/tools/align_imzml.py

@@ -27,7 +27,6 @@ class AlignImzmlMethod(enum.Enum):
     FIRST_MZ_ARR = "FIRST_MZ_ARR"
 
 
-
 class AlignImzml:
     """Aligns the m/z values of an imzml file to a common set of bins."""
 

src/depiction/tools/correct_baseline.py

@@ -46,7 +46,7 @@ def evaluate_file(self, read_file: ImzmlReadFile, write_file: ImzmlWriteFile) ->
             read_file=read_file,
             write_file=write_file,
             operation=self._operation,
-            bind_args=dict(baseline_correction=self._baseline_correction)
+            bind_args=dict(baseline_correction=self._baseline_correction),
         )
 
     def evaluate_spectrum(self, mz_arr: NDArray[float], int_arr: NDArray[float]) -> NDArray[float]:

src/depiction/tools/generate_ion_image.py

@@ -13,6 +13,7 @@
 from depiction.persistence import ImzmlReadFile, ImzmlReader
 from depiction.tools.image_channel_statistics import ImageChannelStatistics
 
+
 class GenerateIonImage:
     """Generates ion images from an imzML file.
 
@@ -21,7 +22,6 @@ class GenerateIonImage:
     it can be expected to be faster than calling the generate_*_for_file methods multiple times.
     """
 
-
     def __init__(self, parallel_config: ParallelConfig) -> None:
         # TODO for peak picked data, it could be worth considering an option to only select the closest peak in case
         #      multiple peaks would fall within the window of interest

src/depiction/tools/normalize_spectra_intensities.py

@@ -18,7 +18,9 @@ class NormalizeSpectraIntensitiesVariant:
 class NormalizeSpectraIntensities:
     variant: NormalizeSpectraIntensitiesVariant
 
-    def process_file(self, read_file: ImzmlReadFile, write_file: ImzmlWriteFile, parallel_config: ParallelConfig) -> None:
+    def process_file(
+        self, read_file: ImzmlReadFile, write_file: ImzmlWriteFile, parallel_config: ParallelConfig
+    ) -> None:
         write_parallel = WriteSpectraParallel.from_config(parallel_config)
         write_parallel.map_chunked_to_file(
             read_file=read_file,

src/depiction/visualize/visualize_2d_channels.py

@@ -1,14 +1,14 @@
 # TODO delete this file if not needed anymore
-#from typing import Optional, Callable, Sequence
+# from typing import Optional, Callable, Sequence
 #
-#from matplotlib import pyplot as plt
+# from matplotlib import pyplot as plt
 #
-#from ion_mapper.image.sparse_image_2d import SparseImage2d
+# from ion_mapper.image.sparse_image_2d import SparseImage2d
 #
 #
 ## TODO the configuration of intensity transformation needs to be more generic / standardized
 #
-#class Visualize2dChannels:
+# class Visualize2dChannels:
 #    """Visualizes 2D image channels."""
 #
 #    def __init__(self, image: SparseImage2d):
@@ -57,4 +57,4 @@
 #        axs: Optional[NDArray[plt.Axes]] = None,
 #    ) -> tuple[plt.Figure, plt.Axes]:
 #        pass
-#
+#

src/depiction/visualize/visualize_mass_shift_map.py

@@ -99,8 +99,7 @@ def _plot_row(
 
         # plot the map
         PlotImage(correction_image).plot_single_channel_image(
-            correction_image.channel_names[0],
-            ax=ax_map, cmap="coolwarm", vmin=-abs_perc, vmax=abs_perc
+            correction_image.channel_names[0], ax=ax_map, cmap="coolwarm", vmin=-abs_perc, vmax=abs_perc
         )
         ax_map.set_title(f"Error for {name}")
         ax_map.axis("off")