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Goodman-lab / DP5

Python workflow for DP5 and DP4 analysis of organic molecules
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Proton_processing.py problem #76

Closed xhliu7 closed 1 year ago

xhliu7 commented 1 year ago

Hi all, I got the following error message when runing the PyDP4.py: Traceback (most recent call last): File "/home/drugdb/PycharmProjects/DP5/./PyDP4_GUI.py", line 2600, in runPyDP4 self.NMRData, self.Isomers, self.settings, self.DP4Data,self.DP5Data = PyDP4.main(ui.table_widget.Tab1.settings) File "/home/drugdb/PycharmProjects/DP5/PyDP4.py", line 397, in main NMRData = NMR.NMRData(settings) File "/home/drugdb/PycharmProjects/DP5/NMR.py", line 73, in init self.ProcessProton(settings,ind1) File "/home/drugdb/PycharmProjects/DP5/NMR.py", line 213, in ProcessProton = process_proton(NMR_file, settings,self.Type) File "/home/drugdb/PycharmProjects/DP5/Proton_processing.py", line 52, in process_proton peak_regions, grouped_peaks, sim_regions, integral_sum, cummulative_vectors, integrals, number_of_protons_structure, optimum_proton_number, total_integral = find_integrals( File "/home/drugdb/PycharmProjects/DP5/Proton_processing.py", line 1709, in find_integrals grouped_peaks, integrals, peak_regions, pickedpeaks, impurities, sim_regions,rounded_integrals = remove_impurities(integrals, File "/home/drugdb/PycharmProjects/DP5/Proton_processing.py", line 1569, in remove_impurities peak_regions = np.delete(peak_regions, to_remove) File "<__array_function__ internals>", line 200, in delete File "/usr/local/lib/python3.10/dist-packages/numpy/lib/function_base.py", line 5126, in delete arr = asarray(arr) ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (32,) + inhomogeneous part.

It seemed that was caused by numpy (I am using 1.24.2) which do not allowed to create an array from "ragged" sequences. But how can I fix this? By the way, I am runing python 3.10.6 on Ubuntu 22.04.1. And the following packages were installed: Package Version

apturl 0.5.2 asteval 0.9.28 bcrypt 3.2.0 blinker 1.4 Brlapi 0.8.3 certifi 2020.6.20 chardet 4.0.0 click 8.0.3 colorama 0.4.4 command-not-found 0.3 contourpy 1.0.7 cryptography 3.4.8 cupshelpers 1.0 cycler 0.11.0 Cython 0.29.33 dbus-python 1.2.18 defer 1.0.6 dill 0.3.6 distro 1.7.0 distro-info 1.1build1 duplicity 0.8.21 fasteners 0.14.1 fonttools 4.38.0 future 0.18.2 httplib2 0.20.2 idna 3.3 importlib-metadata 4.6.4 jeepney 0.7.1 keyring 23.5.0 kiwisolver 1.4.4 language-selector 0.1 launchpadlib 1.10.16 lazr.restfulclient 0.14.4 lazr.uri 1.0.6 lmfit 1.1.0 lockfile 0.12.2 louis 3.20.0 macaroonbakery 1.3.1 Mako 1.1.3 MarkupSafe 2.0.1 matplotlib 3.6.3 monotonic 1.6 more-itertools 8.10.0 multiprocess 0.70.14 netifaces 0.11.0 nmrglue 0.9 numpy 1.24.2 oauthlib 3.2.0 olefile 0.46 packaging 23.0 pandas 1.5.3 paramiko 2.9.3 pathos 0.3.0 patsy 0.5.3 pexpect 4.8.0 Pillow 9.0.1 pip 22.0.2 pox 0.3.2 ppft 1.7.6.6 protobuf 3.12.4 ptyprocess 0.7.0 pycairo 1.20.1 pycups 2.0.1 PyGObject 3.42.1 PyJWT 2.3.0 pymacaroons 0.13.0 PyNaCl 1.5.0 pyparsing 2.4.7 PyQt5 5.15.8 PyQt5-Qt5 5.15.2 PyQt5-sip 12.11.1 pyRFC3339 1.1 python-apt 2.4.0 python-dateutil 2.8.1 python-debian 0.1.43ubuntu1 pytz 2022.1 pyxdg 0.27 PyYAML 5.4.1 qml 0.4.0.27 rdkit 2022.9.4 reportlab 3.6.8 requests 2.25.1 scipy 1.10.0 screen-resolution-extra 0.0.0 SecretStorage 3.3.1 setuptools 59.6.0 six 1.16.0 ssh-import-id 5.11 statsmodels 0.13.5 systemd-python 234 ubuntu-advantage-tools 27.12 ubuntu-drivers-common 0.0.0 ufw 0.36.1 unattended-upgrades 0.1 uncertainties 3.1.7 urllib3 1.26.5 usb-creator 0.3.7 wadllib 1.3.6 wheel 0.37.1 xdg 5 xkit 0.0.0 zipp 1.0.0

xhliu7 commented 1 year ago

It's ok now. I fixed the problem by adding the following 3 lines of code in line 1568,1570,1572 respectively: peak_regions = np.array(peak_regions, dtype=object) grouped_peaks = np.array(grouped_peaks, dtype=object) sim_regions = np.array(sim_regions, dtype=object)