Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

feat: store scan rate and spectrum direction (#196) #204

Merged
merged 1 commit into from
Jun 25, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

This backend web service provides NMR/IR/MS processing for jcamp/RAW/mzML files.

![GitHub release (release name instead of tag name)](https://img.shields.io/github/v/release/ComPlat/chem-spectra-app?include_prereleases&label=version)
![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)
![Testing](https://github.com/ComPlat/chem-spectra-app/actions/workflows/unit_test.yml/badge.svg)

Expand Down
12 changes: 12 additions & 0 deletions chem_spectra/lib/composer/ni.py
Original file line number Diff line number Diff line change
Expand Up @@ -166,6 +166,17 @@ def __get_xy_of_peak(self, peak):
y = peak['y'] or ''
return x, y

def __gen_cyclic_voltammetry_medadata(self):
scan_rate = self.core.dic.get('SCANRATE', [0.1])[0]
x_values = self.core.xs
spectrum_direction = ''
if len(x_values) > 2:
spectrum_direction = 'NEGATIVE' if x_values[0] > x_values[1] else 'POSITIVE'
return [
f"##$CSSCANRATE={scan_rate}\n",
f"##$CSSPECTRUMDIRECTION={spectrum_direction}\n"
]

def __gen_cyclic_voltammetry_data_peaks(self):
content = ['##$CSCYCLICVOLTAMMETRYDATA=\n']
if self.core.is_cyclic_volta:
Expand Down Expand Up @@ -245,6 +256,7 @@ def __compose(self):
meta.extend(self.gen_simulation_info())
if self.core.is_cyclic_volta:
meta.extend(self.__gen_header_cyclic_voltammetry())
meta.extend(self.__gen_cyclic_voltammetry_medadata())
meta.extend(self.__gen_cyclic_voltammetry_data_peaks())
meta.extend(self.gen_ending())

Expand Down
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@

setup(
name='chem-spectra-app',
version='1.2.1',
version='1.2.2',
packages=find_packages(),
include_package_data=True,
zip_safe=False,
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
##DATA CLASS=XYPOINTS
##ORIGIN=
##OWNER=
##SCAN_RATE=0.09
##FIRSTX=1.49048
##LASTX=1.50049
##MINX=-1.9005
Expand Down
2 changes: 2 additions & 0 deletions tests/test_cyclic_volta.py
Original file line number Diff line number Diff line change
Expand Up @@ -28,4 +28,6 @@ def test_cv_compose():
nicv = JcampNIConverter(jbcv)
nicmpsr = NIComposer(nicv)
assert "$$ === CHEMSPECTRA CYCLIC VOLTAMMETRY ===\n" in nicmpsr.meta
assert "##$CSSCANRATE=0.09\n" in nicmpsr.meta
assert "##$CSSPECTRUMDIRECTION=NEGATIVE\n" in nicmpsr.meta
assert "##$CSCYCLICVOLTAMMETRYDATA=\n" in nicmpsr.meta
2 changes: 0 additions & 2 deletions tests/test_ms.py
Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,6 @@ def test_ms_mzml_converter_composer():

lines = mscp.tf_jcamp().read()[:800] \
.decode('utf-8', errors='ignore').split('\n')

print(lines)

assert '##$CSSCANAUTOTARGET=24' in lines
assert '##$CSSCANEDITTARGET=24' in lines
Expand Down
Loading