Error opening 3-D NumPy Masked Array in variable explorer window

[darwin-cai]

Description

What steps will reproduce the problem?

Error description

Spyder version: 5.1.5 Python 3.8 I want to open a masked 3-D NumPy Array in the variable explorer window, but Spyder prompts an error message, Inner Error. In the previous version of Spyder (e.g., 5.0.5), a masked 3-D array can be opened.

Traceback

Traceback (most recent call last):
  File "D:\ProgramData\Anaconda3\lib\site-packages\spyder\plugins\variableexplorer\widgets\collectionsdelegate.py", line 176, in createEditor
    if not editor.setup_and_check(value, title=key, readonly=readonly):
  File "D:\ProgramData\Anaconda3\lib\site-packages\spyder\plugins\variableexplorer\widgets\arrayeditor.py", line 772, in setup_and_check
    btn_layout_top.addWidget(self.shape_label)
AttributeError: 'ArrayEditor' object has no attribute 'shape_label'

Versions

• Spyder version: 5.1.5
• Python version: 3.8.5
• Qt version: 5.9.7
• PyQt5 version: 5.9.2
• Operating System: Windows 7

Dependencies

# Mandatory:
atomicwrites >=1.2.0          :  1.4.0 (OK)
chardet >=2.0.0               :  4.0.0 (OK)
cloudpickle >=0.5.0           :  2.0.0 (OK)
cookiecutter >=1.6.0          :  1.7.2 (OK)
diff_match_patch >=20181111   :  20200713 (OK)
intervaltree >=3.0.2          :  3.1.0 (OK)
IPython >=7.6.0               :  7.29.0 (OK)
jedi >=0.17.2;<0.19.0         :  0.18.0 (OK)
jsonschema >=3.2.0            :  3.2.0 (OK)
keyring >=17.0.0              :  23.1.0 (OK)
nbconvert >=4.0               :  6.1.0 (OK)
numpydoc >=0.6.0              :  1.1.0 (OK)
paramiko >=2.4.0              :  2.7.2 (OK)
parso >=0.7.0;<0.9.0          :  0.8.2 (OK)
pexpect >=4.4.0               :  4.8.0 (OK)
pickleshare >=0.4             :  0.7.5 (OK)
psutil >=5.3                  :  5.8.0 (OK)
pygments >=2.0                :  2.10.0 (OK)
pylint >=2.5.0;<2.10.0        :  2.9.6 (OK)
pyls_spyder >=0.4.0           :  0.4.0 (OK)
pylsp >=1.2.2;<1.3.0          :  1.2.4 (OK)
pylsp_black >=1.0.0           :  None (OK)
qdarkstyle =3.0.2             :  3.0.2 (OK)
qstylizer >=0.1.10            :  0.1.10 (OK)
qtawesome >=1.0.2             :  1.0.2 (OK)
qtconsole >=5.1.0             :  5.1.1 (OK)
qtpy >=1.5.0                  :  1.10.0 (OK)
rtree >=0.9.7                 :  0.9.7 (OK)
setuptools >=49.6.0           :  58.0.4 (OK)
sphinx >=0.6.6                :  4.2.0 (OK)
spyder_kernels >=2.1.1;<2.2.0 :  2.1.3 (OK)
textdistance >=4.2.0          :  4.2.1 (OK)
three_merge >=0.1.1           :  0.1.1 (OK)
watchdog >=0.10.3             :  2.1.3 (OK)
zmq >=17                      :  22.2.1 (OK)

# Optional:
cython >=0.21                 :  None (OK)
matplotlib >=2.0.0            :  3.4.1 (OK)
numpy >=1.7                   :  1.21.2 (OK)
pandas >=1.1.1                :  1.2.4 (OK)
scipy >=0.17.0                :  1.7.0 (OK)
sympy >=0.7.3                 :  None (OK)

[darwin-cai]

Problem solved

I have fixed the error by editing the source file "spyder/plugins/variableexplorer/widgets/arrayeditor.py" after line 718. After adding the code within elif data.ndim == 3: to elif is_masked_array:, detailed changes are as follows:

in script arrayeditor.py start line: 712

elif is_masked_array:
    self.stack.addWidget(ArrayEditorWidget(self, data, readonly,
                                                   xlabels, ylabels))
    self.stack.addWidget(ArrayEditorWidget(self, data.data, readonly,
                                                   xlabels, ylabels))
    self.stack.addWidget(ArrayEditorWidget(self, data.mask, readonly,
                                                   xlabels, ylabels))
    #! -----------------modify start-----------------
    # QSpinBox
    self.index_spin = QSpinBox(self, keyboardTracking=False)
    self.index_spin.valueChanged.connect(self.change_active_widget)

    # Labels
    self.shape_label = QLabel()
    self.slicing_label = QLabel()

    # Set the widget to display when launched
    self.current_dim_changed(self.last_dim)
    #! -----------------modify end-----------------
elif data.ndim == 3:
    # We create here the necessary widgets for current_dim_changed to
    # work. The rest are created below.
    # QSpinBox
    self.index_spin = QSpinBox(self, keyboardTracking=False)
    --snip--

[dalthviz]

Hi @DeevenCai thank you for the feedback! Could you give an example code that triggers this error for you? Also, as you already implemented a fix for this, would you like to submit a PR with your proposed changes?

Just in case, if you want to submit your fix our contribution guide could help (https://github.com/spyder-ide/spyder/blob/5.x/CONTRIBUTING.md) using as base branch the 5.x branch. If you have any doubt let us know!

[darwin-cai]

Thanks for your @dalthviz response. The example code is as follows:

# -*- coding: utf-8 -*-
from netCDF4 import Dataset
ncfile = r'D:\Data\GLASS\GLASS10B02.FVC.1982.nc'
ncid = Dataset(ncfile, 'r')
months = ncid['time'][:]    # read time dimension
lon, lat = ncid['lon'][:], ncid['lat'][:]    # read longitude and latitude dimension
fvc = ncid['FVC'][:]    # read main variable data, which is a 3-Dim NumPy Masked Array, in dim (time, lat, lon)
ncid.close()    # close the handle

Then, the variable fvc is collected by the Variable Explorer Window of Spyder. I clicked fvc in the Variable explorer window to see what the data looks like, but the Error window was prompted as previously reported. So I checked the source code and modified some of them.

In later use of the Variable Explorer Window to show NumPy Masked Array, more errors occurred. I found that there are many bugs for showing masked array in the variable explorer window (an example given below), therefore, attention should be paid to such issues.

---

Bug Example

code file: spyder\plugins\variableexplorer\widgets\arrayeditor.py start line: 889 function: def current_dim_changed(self, index) error in line 895: string_size = ['%i']*3 correction: string_size = ['%i']*self.data.ndim

---

I think the dimensions should change with input arrays, not a fixed number 3. Similar errors may occur in lines 866, 874, I am not sure am I right.

As for contributing to Spyder, I can't do anything because I have no experience in software development. I am sorry for this. Thank you guys for your hard work to maintain Spyder.

[dalthviz]

Thank you @DeevenCai for the new info and the testing you did! Just in case, I was able to reproduce this with this code too:

import numpy as np

x = np.ma.array([[[1]], [[2]], [[3]]])

[PlusUltra2021]

Thank you @DeevenCai, the 3-D masked array can be double-click-viewed after your modification in file "arrayeditor.py"! However, a side effect is that the 1-D & 2-D masked array CAN'T be viewed with a Spyder error popup . 😂 (And after I remove the modification and restart Spyder, the 1-D & 2-D masked array can be viewed like before.) Hope there to be a final solution to this~

[dalthviz]

Hi @PlusUltra2021 maybe you could try the solution at https://github.com/spyder-ide/spyder/pull/16919 . Let us know if that covers all the cases (1-D, 2-D, 3-D)