From da97c6818f5d1ac320e18132c543217d3de20374 Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Thu, 30 May 2024 10:36:44 +0200 Subject: [PATCH] minor changes --- README.md | 26 +++++++++++++------------- examples/spectra_calibration.py | 7 ++++--- 2 files changed, 17 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 43b50de..7d006cb 100644 --- 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 index ce634c8..4e08782 100644 --- 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)