jmrohwer
commented
1 year ago I see you are using a separate conda environment for NMRPy which is great! Actually Python 3.7 has reached end of life and is no longer reported. Can you try to rerecreate the environment with a more recent Python version such as 3.10 or 3.11.
conda create -n nmr python=3.10I realize the documentation uses 3.7 which may be confusing - apologies for that, it was the newest version when that documentation was written. I need to update it :smile: In fact you can use any recent Python version and should definitely stick to a version that is still being actively supported (which currently is 3.8 or higher). To be able to use this for a while, I recommend 3.10 or 3.11.
Ricmelis80
Hy,
When I launch fid_array.calibrate() the follow error appears :
_"--------------------------------------------------------------------------- TraitError Traceback (most recent call last) /tmp/ipykernel_1529787/2848238876.py in
----> 1 fid_array.calibrate()
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/nmrpy/data_objects.py in calibrate(self, fid_number, assign_only_to_index, voff) 1740 aoti=assign_only_to_index, 1741 voff=voff, -> 1742 label=plot_label, 1743 ) 1744
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/nmrpy/plotting.py in init(self, fid_array, y_indices, aoti, voff, lw, label) 1558 title='FidArray calibration', 1559 voff = voff, -> 1560 label=label) 1561 self.peak_selector.process = self.process 1562
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/nmrpy/plotting.py in init(self, data, params, extra_data, extra_data_colour, peaks, ranges, title, voff, label) 1035 1036 self.out = Output() -> 1037 self._make_basic_fig() 1038 1039 self.visible = True
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/nmrpy/plotting.py in _make_basic_fig(self, *args, **kwargs) 1130 plt.ion() 1131 if self._isnotebook(): -> 1132 display(VBox([self.canvas, self.out])) 1133 else: 1134 plt.show()
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/ipywidgets/widgets/widget_box.py in init(self, children, kwargs) 62 def init(self, children=(), kwargs): 63 kwargs['children'] = children ---> 64 super().init(**kwargs) 65 66 @register
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/ipywidgets/widgets/widget.py in init(self, kwargs) 501 """Public constructor""" 502 self._model_id = kwargs.pop('model_id', None) --> 503 super().init(kwargs) 504 505 Widget._call_widget_constructed(self)
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in init(self, *args, **kwargs) 1345 for key, value in kwargs.items(): 1346 if self.has_trait(key): -> 1347 setattr(self, key, value) 1348 changes[key] = Bunch( 1349 name=key,
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in set(self, obj, value) 730 raise TraitError('The "%s" trait is read-only.' % self.name) 731 else: --> 732 self.set(obj, value) 733 734 def _validate(self, obj, value):
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in set(self, obj, value) 704 705 def set(self, obj, value): --> 706 new_value = self._validate(obj, value) 707 try: 708 old_value = obj._trait_values[self.name]
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in _validate(self, obj, value) 736 return value 737 if hasattr(self, "validate"): --> 738 value = self.validate(obj, value) 739 if obj._cross_validation_lock is False: 740 value = self._cross_validate(obj, value)
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in validate(self, obj, value) 2869 return value 2870 -> 2871 value = self.validate_elements(obj, value) 2872 2873 return value
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value) 2881 v = self._trait._validate(obj, v) 2882 except TraitError as error: -> 2883 self.error(obj, v, error) 2884 else: 2885 validated.append(v)
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in error(self, obj, value, error, info) 821 ), 822 ) --> 823 raise error 824 else: 825 # this trait caused an error
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in validate_elements(self, obj, value) 2879 for v in value: 2880 try: -> 2881 v = self._trait._validate(obj, v) 2882 except TraitError as error: 2883 self.error(obj, v, error)
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in _validate(self, obj, value) 736 return value 737 if hasattr(self, "validate"): --> 738 value = self.validate(obj, value) 739 if obj._cross_validation_lock is False: 740 value = self._cross_validate(obj, value)
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in validate(self, obj, value) 2149 return value 2150 else: -> 2151 self.error(obj, value) 2152 2153 def info(self):
~/anaconda3/envs/nmrpy/lib/python3.7/site-packages/traitlets/traitlets.py in error(self, obj, value, error, info) 826 if self.name is None: 827 # this is not the root trait --> 828 raise TraitError(value, info or self.info(), self) 829 else: 830 # this is the root trait
TraitError: The 'children' trait of a VBox instance contains an Instance of a TypedTuple which expected a Widget, not the FigureCanvasAgg at '0x7f8fb0c7b7d0'"_
Here the code I used in jupyter notebook :
_#Import libraries import nmrpy import os from matplotlib import pyplot as plt
Fid array processing
fid_array = nmrpy.from_path('root_folder') fid_array.emhz_fids() fid_array.ft_fids() fid_array.phase_correct_fids() fid_array.real_fids() fid_array.norm_fids() fid_array.plot_array(upper_ppm=1, lower_ppm=-1, filled=True, azim=-76, elev=23) fid_array.calibrate()
Any suggestions? Many thanks!