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Change coordinate integration from raw intensity to area under the curve #24

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Change coordinate integration from raw intensity to area under the curve #24

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696882f
New coordinate integration method first pass
alex-l-kong May 30, 2024
be3d08f
Use intensities of the spectra at the spot and not the total mass df
alex-l-kong May 30, 2024
3b8839a
Make sure to pass in arguments needed for updated coordinate integration
alex-l-kong May 30, 2024
0b97a38
Fix test for coordinate integration
alex-l-kong May 30, 2024
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22 changes: 17 additions & 5 deletions src/maldi_tools/extraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
import pandas as pd
import xarray as xr
from pyimzml.ImzMLParser import ImzMLParser
from scipy import signal
from scipy import integrate, signal
from tqdm.notebook import tqdm

from maldi_tools import plotting
Expand Down Expand Up @@ -232,13 +232,23 @@ def peak_spectra(
return panel_df


def coordinate_integration(peak_df: pd.DataFrame, imz_data: ImzMLParser) -> xr.DataArray:
def coordinate_integration(
peak_df: pd.DataFrame,
l_ips_r: np.ndarray,
r_ips_r: np.ndarray,
peak_widths_height: np.ndarray,
imz_data: ImzMLParser,
) -> xr.DataArray:
"""Integrates the coordinates with the discovered, post-processed peaks and generates an image for
each of the peaks using the imzML coordinate data.

Args:
----
peak_df (pd.DataFrame): The unique peaks from the data.
l_ips_r (np.ndarray): The rounded left (lower) bound.
r_ips_r (np.ndarray): The rounded right (upper) bound.
peak_widths_height (np.ndarray): The height of the contour lines at which the peak widths were
calculated from.
imz_data (ImzMLParser): The imzML object.

Returns:
Expand All @@ -260,10 +270,12 @@ def coordinate_integration(peak_df: pd.DataFrame, imz_data: ImzMLParser) -> xr.D
for idx, (x, y, _) in tqdm(enumerate(imz_data.coordinates), total=len(imz_data.coordinates)):
mzs, intensities = imz_data.getspectrum(idx)

intensity: np.ndarray = intensities[np.isin(mzs, peak_df["m/z"])]

for i_idx, peak in peak_df.loc[peak_df["m/z"].isin(mzs), "peak"].reset_index(drop=True).items():
imgs[peak_dict[peak], x - 1, y - 1] += intensity[i_idx]
left_idx = abs(intensities.values - l_ips_r[i_idx]).idxmin()
right_idx = abs(intensities.values - r_ips_r[i_idx]).idxmin()
imgs[peak_dict[peak], x - 1, y - 1] += integrate.simpson(
intensities.values[left_idx:right_idx]
) - (peak_widths_height * (right_idx - left_idx))

img_data = xr.DataArray(
data=imgs,
Expand Down
10 changes: 8 additions & 2 deletions templates/maldi-pipeline.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -466,7 +466,13 @@
},
"outputs": [],
"source": [
"image_data = extraction.coordinate_integration(peak_df=peak_df, imz_data=imz_data)"
"image_data = extraction.coordinate_integration(\n",
" peak_df=peak_df,\n",
" l_ips_r=l_ips_r,\n",
" r_ips_r=r_ips_r,\n",
" peak_widths_height=peak_widths_height,\n",
" imz_data=imz_data,\n",
")"
]
},
{
Expand Down Expand Up @@ -598,7 +604,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.1"
"version": "3.11.6"
},
"vscode": {
"interpreter": {
Expand Down
11 changes: 10 additions & 1 deletion tests/extraction_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,16 @@ def test_peak_spectra(

def test_coordinate_integration(imz_data, peak_widths):
peak_df, *_ = peak_widths
img_data = extraction.coordinate_integration(peak_df=peak_df, imz_data=imz_data)
l_ips_r = np.arange(0, peak_df.shape[0], 5)
r_ips_r = l_ips_r + 2
peak_widths_height = np.repeat(2, peak_df.shape[0])
img_data = extraction.coordinate_integration(
peak_df=peak_df,
l_ips_r=l_ips_r,
r_ips_r=r_ips_r,
peak_widths_height=peak_widths_height,
imz_data=imz_data,
)

# Make sure the shape of any given image is correct.
assert img_data.shape[1:] == (10, 10)
Expand Down
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