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Merged
carlosbornes merged 1 commit into from
Apr 24, 2025
Merged

Solved problem with convert from and to ppm #12

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27 changes: 17 additions & 10 deletions src/simpyson/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def hz2ppm(hz, b0, nucleus, isotope_file=None):
isotope_file = os.path.join(dir, 'isotope_data.json')

isotope = int(''.join(filter(str.isdigit, nucleus)))
element = ''.join(filter(str.isalpha, nucleus)).upper()
element = ''.join(filter(str.isalpha, nucleus)).capitalize()
b0_unit = ''.join(filter(str.isalpha, b0)).lower()

with open(isotope_file) as f:
Expand All @@ -132,12 +132,16 @@ def hz2ppm(hz, b0, nucleus, isotope_file=None):
raise ValueError(f'Nucleus {nucleus} not found in isotope data.')

if b0_unit == 't':
b0_value = float(''.join(filter(str.isdigit, b0)))
ppm = hz / (b0_value * gamma)
b0_value = float(''.join(filter(lambda x: x.isdigit() or x == '.', b0)))
larm_freq = gamma * 1e7 * b0_value / (2 * np.pi * 1e6)
ppm = hz / np.abs(larm_freq)
elif b0_unit == 'mhz':
b0_value = float(''.join(filter(str.isdigit, b0)))
b0_value = float(''.join(filter(lambda x: x.isdigit() or x == '.', b0)))
gamma_h = data['H']['1']['Gamma']
ppm = hz / (b0_value/(gamma_h/gamma))
b0_value_T = 2 * np.pi * b0_value * 1e6 / (gamma_h * 1e7)
larm_freq = gamma * 1e7 * b0_value_T / (2 * np.pi * 1e6)
# ppm conversion requires absolute value of larm_freq
ppm = hz / np.abs(larm_freq)
else:
raise ValueError('B0 unit must be T or MHz.')

Expand Down Expand Up @@ -165,7 +169,7 @@ def ppm2hz(ppm, b0, nucleus, isotope_file=None):
isotope_file = os.path.join(dir, 'isotope_data.json')

isotope = int(''.join(filter(str.isdigit, nucleus)))
element = ''.join(filter(str.isalpha, nucleus)).upper()
element = ''.join(filter(str.isalpha, nucleus)).capitalize()
b0_unit = ''.join(filter(str.isalpha, b0)).lower()

with open(isotope_file) as f:
Expand All @@ -176,13 +180,16 @@ def ppm2hz(ppm, b0, nucleus, isotope_file=None):
raise ValueError(f'Nucleus {nucleus} not found in isotope data.')

if b0_unit == 't':
b0_value = float(''.join(filter(str.isdigit, b0)))
hz = ppm * (b0_value * gamma)
b0_value = float(''.join(filter(lambda x: x.isdigit() or x == '.', b0)))
larm_freq = gamma * 1e7 * b0_value / (2 * np.pi * 1e6)
elif b0_unit == 'mhz':
b0_value = float(''.join(filter(str.isdigit, b0)))
b0_value = float(''.join(filter(lambda x: x.isdigit() or x == '.', b0)))
gamma_h = data['H']['1']['Gamma']
hz = ppm * (b0_value/(gamma_h/gamma))
b0_value_T = 2 * np.pi * b0_value * 1e6 / (gamma_h * 1e7)
larm_freq = gamma * 1e7 * b0_value_T / (2 * np.pi * 1e6)
else:
raise ValueError('B0 unit must be T or MHz.')

hz = ppm * np.abs(larm_freq)

return hz
50 changes: 49 additions & 1 deletion src/simpyson/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -120,6 +120,10 @@ def create_menu(self):
convert_hz_to_ppm.triggered.connect(self.convert_hz_to_ppm)
process_menu.addAction(convert_hz_to_ppm)

convert_ppm_to_hz = QAction('Convert ppm to Hz', self)
convert_ppm_to_hz.triggered.connect(self.convert_ppm_to_hz)
process_menu.addAction(convert_ppm_to_hz)

convert_fid_to_spe = QAction('Convert FID to SPE', self)
convert_fid_to_spe.triggered.connect(self.convert_fid_to_spe)
process_menu.addAction(convert_fid_to_spe)
Expand Down Expand Up @@ -270,7 +274,7 @@ def convert_hz_to_ppm(self):
file_name = item.text()
file_data = self.files_data[file_name]['data']

if file_data and 'hz' in file_data.data: # Remove the format check
if file_data and 'hz' in file_data.data:
try:
new_data = copy.deepcopy(file_data)
new_data.b0 = b0
Expand All @@ -289,6 +293,50 @@ def convert_hz_to_ppm(self):

self.plot_data(selected_items)

def convert_ppm_to_hz(self):
selected_items = self.file_list.selectedItems()

if not selected_items:
QMessageBox.warning(self, 'Convert ppm to Hz', 'No file selected!')
return

b0, ok_b0 = QInputDialog.getText(self, 'Input', 'Enter B0 (e.g., 400MHz or 9.4T):')
if not (ok_b0 and b0):
return

nucleus, ok_nucleus = QInputDialog.getText(self, 'Input', 'Enter nucleus (e.g., 1H or 13C):')
if not (ok_nucleus and nucleus):
return

for item in selected_items:
file_name = item.text()
file_data = self.files_data[file_name]['data']

if file_data and 'ppm' in file_data.data:
try:
new_data = copy.deepcopy(file_data)
new_data.b0 = b0
new_data.nucleus = nucleus

ppm = new_data.data['ppm']
new_data.data['hz'] = ppm2hz(ppm, b0, nucleus)

# This is just an initial implementation
# Maybe one should implement a way to select on the GUI
# which range to show on the plot
if 'ppm' in new_data.data:
del new_data.data['ppm']

self.files_data[file_name]['data'] = new_data
if file_name == self.current_file:
self.data = new_data

except ValueError as e:
QMessageBox.warning(self, 'Convert ppm to Hz',
f"Error converting {file_name}: {str(e)}")

self.plot_data(selected_items)

def convert_fid_to_spe(self):
selected_items = self.file_list.selectedItems()

Expand Down
25 changes: 5 additions & 20 deletions src/simpyson/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,6 @@ def _read_spe(self):
raise ValueError('Both B0 and nucleus must be specified.')
else:
dir = os.path.dirname(os.path.realpath(__file__))
isotope_file = os.path.join(dir, 'isotope_data.json')
with open(self.filename) as f:
data_sec = False
real = []
Expand All @@ -95,25 +94,11 @@ def _read_spe(self):
imag = np.array(imag)
hz = np.array(hz)

isotope = int(''.join(filter(str.isdigit, self.nucleus)))
element = ''.join(filter(str.isalpha, self.nucleus)).capitalize()

b0_unit = ''.join(filter(str.isalpha, self.b0)).lower()

with open(isotope_file) as f:
data = json.load(f)
gamma = data[element][str(isotope)]['Gamma']

if b0_unit == 't':
b0 = int(''.join(filter(str.isdigit, self.b0)))
ppm = hz / (b0 * gamma)
elif b0_unit == 'mhz':
b0 = int(''.join(filter(str.isdigit, self.b0)))
gamma_h = data['H']['1']['Gamma']
ppm = hz / (b0/(gamma_h/gamma))
else:
raise ValueError('B0 unit must be T or MHz.')
self.data = {'real': real, 'imag': imag, 'np': np_value, 'sw': sw, 'hz': hz, 'ppm': ppm}
try:
ppm = hz2ppm(hz, self.b0, self.nucleus)
self.data = {'real': real, 'imag': imag, 'np': np_value, 'sw': sw, 'hz': hz, 'ppm': ppm}
except ValueError as e:
print(f"Error converting to ppm: {e}")

def _read_fid(self):
"""
Expand Down
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