ScanImage TiffReader not able to read the sample data

[marytunun]

Describe the issue:

1. I successfully installed all the requirements except scanimage-tiff-reader(described later).
2. Was able to open the suite2p GUI and setup the configuration
3. But after i press 'Run' i see this error in the GUI of the suite2p is as follows:

{'data_path': ['C:/Users/Maria/Documents/suite2p/tiffs'], 'subfolders': [], 'save_path0': 'C:/Users/Maria/Documents/suite2p/save_path', 'fast_disk': 'C:/Users/Maria/Documents/suite2p/fast_disk', 'input_format': 'tif'}
tif
** Found 5 tifs - converting to binary **
2000 frames of binary, time 18.01 sec.
4000 frames of binary, time 31.26 sec.
6000 frames of binary, time 42.81 sec.

ERROR<<<
Traceback (most recent call last):
ERROR<<<
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\runpy.py", line 197, in run_module_as_main
ERROR<<<
return run_code(code, main_globals, None,
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\runpy.py", line 87, in run_code
ERROR<<<
exec(code, run_globals)
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\suite2p_main.py", line 78, in
ERROR<<<
main()
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\suite2p_main.py", line 71, in main
run_s2p(ops, db)
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\suite2p\run_s2p.py", line 411, in run_s2p
ERROR<<<
ops0 = io.tiff_to_binary(ops.copy())
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\suite2p\io\tiff.py", line 135, in tiff_to_binary
tif, Ltif = open_tiff(file, use_sktiff)
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\suite2p\io\tiff.py", line 82, in open_tiff
tif = ScanImageTiffReader(file)
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\ScanImageTiffReader_init.py", line 173, in init
ERROR<<<
self.open(filename)
File "C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\ScanImageTiffReader_init_.py", line 222, in open
ERROR<<<
raise Exception(self.__ctx.log.decode("utf-8","strict"))
ERROR<<<
Exception: No strip offsets found. This reader only reads Tiffs with strip data

-----------**********---------------***-----------------------------------------------------------
I suspect that the issue somehow relates to the error that Scanimage-tiff-reader encounters during installation. The package is not able to build a wheel and is installed by the legacy method using setup.py, here is the error:

      ############################
      # Package would be ignored #
      ############################
      Python recognizes 'ScanImageTiffReader.external' as an importable package,
      but it is not listed in the `packages` configuration of setuptools.

      'ScanImageTiffReader.external' has been automatically added to the distribution only
      because it may contain data files, but this behavior is likely to change
      in future versions of setuptools (and therefore is considered deprecated).

      Please make sure that 'ScanImageTiffReader.external' is included as a package by using
      the `packages` configuration field or the proper discovery methods
      (for example by using `find_namespace_packages(...)`/`find_namespace:`
      instead of `find_packages(...)`/`find:`).

      You can read more about "package discovery" and "data files" on setuptools
      documentation page.


  !!

    check.warn(importable)
  C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\setuptools\command\build_py.py:202: SetuptoolsDeprecationWarning:     Installing 'ScanImageTiffReader.external.__pycache__' as data is deprecated, please list it in `packages`.
      !!


      ############################
      # Package would be ignored #
      ############################
      Python recognizes 'ScanImageTiffReader.external.__pycache__' as an importable package,
      but it is not listed in the `packages` configuration of setuptools.

      'ScanImageTiffReader.external.__pycache__' has been automatically added to the distribution only
      because it may contain data files, but this behavior is likely to change
      in future versions of setuptools (and therefore is considered deprecated).

      Please make sure that 'ScanImageTiffReader.external.__pycache__' is included as a package by using
      the `packages` configuration field or the proper discovery methods
      (for example by using `find_namespace_packages(...)`/`find_namespace:`
      instead of `find_packages(...)`/`find:`).

      You can read more about "package discovery" and "data files" on setuptools
      documentation page.


  !!

    check.warn(importable)
  copying src\ScanImageTiffReader\__init__.pyc -> build\lib\ScanImageTiffReader
  creating build\lib\ScanImageTiffReader\__pycache__
  copying src\ScanImageTiffReader\__pycache__\__init__.cpython-36.pyc -> build\lib\ScanImageTiffReader\__pycache__
  copying src\ScanImageTiffReader\__pycache__\__init__.cpython-37.pyc -> build\lib\ScanImageTiffReader\__pycache__
  creating build\lib\ScanImageTiffReader\external
  copying src\ScanImageTiffReader\external\README.md -> build\lib\ScanImageTiffReader\external
  copying src\ScanImageTiffReader\external\__init__.py -> build\lib\ScanImageTiffReader\external
  copying src\ScanImageTiffReader\external\__init__.pyc -> build\lib\ScanImageTiffReader\external
  creating build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin
  creating build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib
  copying src\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib\libScanImageTiffReaderAPI.so -> build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib
  creating build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Linux
  creating build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Linux\lib
  copying src\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Linux\lib\libScanImageTiffReaderAPI.so -> build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Linux\lib
  creating build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-win64
  creating build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-win64\lib
  copying src\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-win64\lib\ScanImageTiffReaderAPI.dll -> build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-win64\lib
  creating build\lib\ScanImageTiffReader\external\__pycache__
  copying src\ScanImageTiffReader\external\__pycache__\__init__.cpython-36.pyc -> build\lib\ScanImageTiffReader\external\__pycache__
  copying src\ScanImageTiffReader\external\__pycache__\__init__.cpython-37.pyc -> build\lib\ScanImageTiffReader\external\__pycache__
  C:\Users\Maria\anaconda3\envs\suite2p\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
    warnings.warn(
  installing to build\bdist.win-amd64\wheel
  running install
  running install_lib
  creating build\bdist.win-amd64
  creating build\bdist.win-amd64\wheel
  creating build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data
  creating build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib
  creating build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader
  creating build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader\external
  copying build\lib\ScanImageTiffReader\external\README.md -> build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader\external
  creating build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin
  creating build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib
  copying build\lib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib\libScanImageTiffReaderAPI.so -> build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib
  error: could not create 'build\bdist.win-amd64\wheel\scanimage_tiff_reader-1.4.1.data\purelib\ScanImageTiffReader\external\ScanImageTiffReader-1.4.1-Darwin\lib\libScanImageTiffReaderAPI.so': No such file or directory
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for scanimage-tiff-reader
Running setup.py clean for scanimage-tiff-reader
Failed to build scanimage-tiff-reader
Installing collected packages: scanimage-tiff-reader
Running setup.py install for scanimage-tiff-reader ... done
DEPRECATION: scanimage-tiff-reader was installed using the legacy 'setup.py install' method, because a wheel could not be built for it. pip 23.1 will enforce this behaviour change. A possible replacement is to fix the wheel build issue reported above. Discussion can be found at pypa/pip#8368

Provide environment info:

active environment : suite2p
active env location : C:\Users\Maria\anaconda3\envs\suite2p
shell level : 2
user config file : C:\Users\Maria.condarc
populated config files : C:\Users\Maria.condarc
conda version : 23.1.0
conda-build version : 3.23.3
python version : 3.10.9.final.0
virtual packages : __archspec=1=x86_64
__win=0=0
base environment : C:\Users\Maria\anaconda3 (writable)
conda av data dir : C:\Users\Maria\anaconda3\etc\conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/win-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/win-64
https://repo.anaconda.com/pkgs/r/noarch
https://repo.anaconda.com/pkgs/msys2/win-64
https://repo.anaconda.com/pkgs/msys2/noarch
package cache : C:\Users\Maria\anaconda3\pkgs
C:\Users\Maria.conda\pkgs
C:\Users\Maria\AppData\Local\conda\conda\pkgs
envs directories : C:\Users\Maria\anaconda3\envs
C:\Users\Maria.conda\envs
C:\Users\Maria\AppData\Local\conda\conda\envs
platform : win-64
user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Windows/10 Windows/10.0.17763
administrator : False
netrc file : None
offline mode : False

-------------------------**********************-------------------------------*****************************---------------
To solve the wheel building issue of the imagescan-tiff-reader, i also have installed (following this thread https://stackoverflow.com/questions/71470989/python-setup-py-bdist-wheel-did-not-run-successfully):
nes-py
Cmake

[carsen-stringer]

Sorry this library needs to update, we've removed this dependency for now, please pip install git+https://GitHub.com/mouseland/suite2p.git