I'm trying to compile a python application using Pyinstaller with the following spec file:

# -*- mode: python ; coding: utf-8 -*-


a = Analysis(
    ['src\\cdi_live.py'],
    pathex=['src', 'venv/Lib/site-packages'],
    binaries=[],
    datas=[
        ('example_data/*.tif', 'example_data'),
        ('LICENSE.txt', '.'),
        ('README.md', '.')
    ],
    hiddenimports=[],
    hookspath=[],
    hooksconfig={},
    runtime_hooks=[],
    excludes=[],
    noarchive=False,
)
pyz = PYZ(a.pure)

exe = EXE(
    pyz,
    a.scripts,
    [],
    exclude_binaries=True,
    name='cdi_live',
    debug="all",
    bootloader_ignore_signals=False,
    strip=False,
    upx=True,
    console=True,
    disable_windowed_traceback=False,
    argv_emulation=False,
    target_arch=None,
    codesign_identity=None,
    entitlements_file=None,
)
coll = COLLECT(
    exe,
    a.binaries,
    a.datas,
    strip=False,
    upx=True,
    upx_exclude=[],
    name='cdi_live',
)

When I run Pyinstaller on this, it works exactly as expected. No red flags while compiling, and the output goes into my dist directory. When I run the executable, a terminal opens up, I get my verbose debugging messages, and then my GUI opens on top of that. Everything in the application functions perfectly, and I breathe a sigh of relief.

Then, because I don't want to open a console every time I run my application, I change one line in the spec file:

exe = EXE(
   ...
   console=False,
   ...
)

I run Pyinstaller again. At first, it seems to have worked again. But when I run the executable, I get a message saying that it failed to execute the script due to an unhandled AttributeError when I imported scipy.ndimage (full traceback given below).

Why would that single line cause the compiled executable to fail, and how do I fix it?

Additional information

I don't know how much of this will be useful, but I'll include everything I think might have bearing on the question.

I've gone back and forth with the console option and it always works with console=True and always fails with console=False.

I've used the same spec file to compile this app in the past, and it worked fine. Since the previous version, I've added some matplotlib.backends.backend_tkagg.FigureCanvasTkAgg widgets.

The traceback that shows up in the error pop-up is long and burrows deep into the dependencies:

Traceback (most recent call last):
  File "cdi_live.py", line 20, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "phasing.py", line 7, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "scipy\ndimage\__init__.py", line 152, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "scipy\ndimage\_filters.py", line 37, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "scipy\_lib\_util.py", line 18, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "scipy\_lib\_array_api.py", line 21, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "scipy\_lib\array_api_compat\numpy\__init__.py", line 1, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "numpy\f2py\__init__.py", line 19, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "numpy\f2py\f2py2e.py", line 23, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "numpy\f2py\crackfortran.py", line 159, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "numpy\f2py\auxfuncs.py", line 19, in <module>
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 378, in exec_module
  File "numpy\f2py\cfuncs.py", line 19, in <module>
AttributeError: 'NoneType' object has no attribute 'write'

The last call to my own code (File "phasing.py", line 7, in <module>) is an attempt to import scipy.ndimage. Before that point, python has already imported tkinter, numpy, and several packages from matplotlib.

Running the EXE with a debugger active doesn't provide much help. The output is identical to the console output. After I close out the error message, I get a few additional lines:

00000047    33.55646133 [31580] [PYI-31580:DEBUG] LOADER: ERROR.    
00000048    33.55653381 [31580] [PYI-31580:DEBUG] LOADER: cleaning up Python interpreter... 
00000049    33.63221741 [31580] [PYI-31580:DEBUG] LOADER: unloading Python shared library...    
00000050    33.63228989 [31580] [PYI-31580:DEBUG] LOADER: end of process reached!

Pyinstaller: executable only runs when `console=True`

Additional information