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fix: data normalization and improve handling of runs in JcampMSConverter #220

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merged 4 commits into from
Nov 28, 2024
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fix: data normalization and improve handling of runs in JcampMSConverter #220

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ce636ac
Fix data normalization and improve handling of runs in JcampMSConverter
Nicolass67 Nov 22, 2024
6ccc252
Add unit test for JCAMP single point handling in the last line
Nicolass67 Nov 25, 2024
37ca0f6
Update requirements.txt to use specific branch of nmrglue
Nicolass67 Nov 25, 2024
7980453
Change nmrglue version for unit test in CI
Nicolass67 Nov 25, 2024
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12 changes: 10 additions & 2 deletions chem_spectra/lib/converter/jcamp/ms.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from chem_spectra.lib.converter.jcamp.data_parse import make_ms_data_xsys
from chem_spectra.lib.converter.share import reduce_pts
import numpy as np

MARGIN = 1
THRESHOLD_MS = 0.05
Expand Down Expand Up @@ -78,12 +79,19 @@ def __get_ratio(self, spc):

return ratio, noise_ratio

# Guarantees that the data passed to `reduce_pts` and subsequent operations
# conforms to the expected structure.
def __normalize_data(self, data):
if isinstance(data, np.ndarray) and data.ndim == 3 and data.shape[0] == 1:
return data[0]
return data

def __decode(self, runs):
spectra = []
best_ratio, best_idx, backup_ratio, backup_idx = 0, 0, 0, 0
for idx, data in enumerate(runs):
data = self.__normalize_data(data)
spectra.append(reduce_pts(data))

ratio, noise_ratio = self.__get_ratio(data)
if (best_ratio < ratio) and (noise_ratio <= 50.0):
best_idx = idx
Expand Down Expand Up @@ -117,4 +125,4 @@ def __set_datatables(self):
)
)
dts.append({'dt': dt, 'pts': pts})
return dts
return dts
2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -88,5 +88,5 @@ dependencies:
- werkzeug==3.0.3
- wrapt==1.16.0
- zipp==3.19.2
- -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
- -e git+https://github.com/ComPlat/nmrglue.git@Refactor-parse_xy_xy-standardize-output-3D-arrays#egg=nmrglue
prefix: /home/eln/anaconda3/envs/python-v38
2 changes: 1 addition & 1 deletion requirements.txt
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Expand Up @@ -19,7 +19,7 @@ matplotlib==3.7.3
mccabe==0.6.1
more-itertools==7.2.0
# -e git+https://github.com/ComPlat/nmrglue.git@e6e8a63b1848ae0525f07de0a6ec0cfdb900ba60#egg=nmrglue
-e git+https://github.com/ComPlat/nmrglue.git@stable_version#egg=nmrglue
-e git+https://github.com/ComPlat/nmrglue.git@Refactor-parse_xy_xy-standardize-output-3D-arrays#egg=nmrglue
netCDF4==1.5.3
numpy==1.22.4
olefile==0.46
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