minor changes

fgcz · May 30, 2024 · da97c68 · da97c68
1 parent 98abb95
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diff --git a/README.md b/README.md
@@ -3,19 +3,19 @@
 A lot of the files and folders are in a early development state or may require some serious refactoring.
 For now, I give a summary of the modules which are somewhat stable already:
 
-| Module                               | Description                                                                |
-|--------------------------------------|----------------------------------------------------------------------------|
-| `ionplotter.spectrum`                | Collection of spectra processing functionality.                            |
-| `ionplotter.spectrum.baseline`       | Estimate spectrum baseline curve.                                          |
-| `ionplotter.spectrum.peak_picking`   |                                                                            |
-| `ionplotter.spectrum.peak_filtering` |                                                                            |
-| `ionplotter.calibration`             | Calibration specific functionality.                                        |
-| `ionplotter.image`                   | Image specific functionality.                                              |
-| `ionplotter.parallel_ops`            | Basic building blocks for parallelization of operations across *ReadFiles. |
-| `ionplotter.persistence`             | Persistence specific code, including reader and writer for Imzml files.    |
-| `ionplotter.peak_filtering`          | Peak filtering specific code.                                              |
-| `ionplotter.peak_picking`            | Peak picking specific code.                                                |
-| `ionplotter.visualize`               | Visualization specific code.                                               |
+| Module                              | Description                                                                |
+|-------------------------------------|----------------------------------------------------------------------------|
+| `depiction.spectrum`                | Collection of spectra processing functionality.                            |
+| `depiction.spectrum.baseline`       | Estimate spectrum baseline curve.                                          |
+| `depiction.spectrum.peak_picking`   |                                                                            |
+| `depiction.spectrum.peak_filtering` |                                                                            |
+| `depiction.calibration`             | Calibration specific functionality.                                        |
+| `depiction.image`                   | Image specific functionality.                                              |
+| `depiction.parallel_ops`            | Basic building blocks for parallelization of operations across *ReadFiles. |
+| `depiction.persistence`             | Persistence specific code, including reader and writer for Imzml files.    |
+| `depiction.peak_filtering`          | Peak filtering specific code.                                              |
+| `depiction.peak_picking`            | Peak picking specific code.                                                |
+| `depiction.visualize`               | Visualization specific code.                                               |
 
 ## Setup dev environment
 

diff --git a/examples/spectra_calibration.py b/examples/spectra_calibration.py
@@ -1,6 +1,5 @@
 from pathlib import Path
-import spectrum_utils.spectrum
-import spectrum_utils.plot
+
 from matplotlib import pyplot as plt
 from numpy.typing import NDArray
 from xarray import DataArray
@@ -53,7 +52,8 @@ def main() -> None:
     print("Applying models...")
     spectra_calib = []
     for (mz_arr, int_arr), features in zip(spectra_picked, all_features):
-        mz_arr, int_arr = calib.apply_spectrum_model(spectrum_mz_arr=mz_arr, spectrum_int_arr=int_arr, model_coef=features)
+        mz_arr, int_arr = calib.apply_spectrum_model(spectrum_mz_arr=mz_arr, spectrum_int_arr=int_arr,
+                                                     model_coef=features)
         spectra_calib.append((mz_arr, int_arr))
 
     # compare the spectra somehow...
@@ -77,6 +77,7 @@ def main() -> None:
     ax.set_ylim(0, 1)
     plt.show()
 
+
 def create_data():
     original_file = "/Users/leo/code/msi/code/msi_targeted_preproc/example/data-work/menzha_20231208_s607930_64074-b20-30928-a/baseline_adj.imzML"
     imzml_file = ImzmlReadFile(original_file)