flika-org/flika

An interactive image processing program for biologists written in Python.

flika's Issues

Cannot open flika on macOS Catalina

I am using a mac with macOS Catalina. I am using anaconda to access python. In the terminal, I typed "pip install flika" as directed. Then, I typed "ipython". Finally, I typed "from flika import *", then "start_flika()". Up to this point everything is okay. However, after clicking return, I get a long string a text that ends with the following: KeyError: 'Unknown configuration option "useWeave"'. Could you please help? I attached the code in a Word document.
error.docx

function Logger._send_report() not yet implemented

pyside?? pyside2?? impossible situation?

on a CentOS cluster,trying to install for a user. Using anaconda/3.6-5.0.1 as a base, all deps installed
(see http://termbin.com/fric )
except for pyside, which is no longer available for versions > 3.4.:

pip install flika
...
only these python versions are supported: [(2, 6), (2, 7), (3, 2), (3, 3), (3, 4)] 
...

And pyside2 is not integrated into flika. What do you recommend for resolving this impasse?

When trying to start flika with the above deps installed (tho not pyside; apparently not a stated dep):

$ flika
2018-11-05 20:52:15,545 - ERROR - Uncaught exception
Traceback (most recent call last):
  File "/data/apps/anaconda/3.6-5.0.1/lib/python3.6/site-packages/qtpy/__init__.py", line 148, in <module>
    from PySide import __version__ as PYSIDE_VERSION  # analysis:ignore
ModuleNotFoundError: No module named 'PySide'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/data/apps/anaconda/3.6-5.0.1/bin/flika", line 7, in <module>
    from flika.flika import exec_
  File "/data/apps/anaconda/3.6-5.0.1/lib/python3.6/site-packages/flika/__init__.py", line 4, in <module>
    from .flika import start_flika
  File "/data/apps/anaconda/3.6-5.0.1/lib/python3.6/site-packages/flika/flika.py", line 12, in <module>
    from .app.application import FlikaApplication
  File "/data/apps/anaconda/3.6-5.0.1/lib/python3.6/site-packages/flika/app/application.py", line 9, in <module>
    from qtpy import QtCore, QtWidgets, QtGui
  File "/data/apps/anaconda/3.6-5.0.1/lib/python3.6/site-packages/qtpy/__init__.py", line 154, in <module>
    raise PythonQtError('No Qt bindings could be found')
qtpy.PythonQtError: No Qt bindings could be found

The pyqt is yet another problem, but I haven't started in on that. Waiting to see if the pyside bit is addressable.

thanks
Harry

PolyLine selector fails on remove link

Traceback (most recent call last):
File "flika\flika\roi.py", line 814, in removeSegment
self.lines.remove(segment)
ValueError: list.remove(x): x not in list

viewing n-dimensional array

Light sheet microscopy often generates 4D datasets, where a single timepoint is a volume. It would be awesome if flika could support these datasets (and potentially 5-dimensional data, e.g. [time, trial, z, y, x]).
Supporting these data would require a) generating an axis slider for each non-color axis beyond the first 2, and b) some way for the user to define which axis is time.

I'm not familiar enough with flika/pyqtgraph internals to submit a PR for this yet, but if there was a working PR for this would it be something the flika devs would be interested in?

Kymograph update function fails on out of bounds

Traceback (most recent call last):
File "flika\flika\roi.py", line 432, in update_kymograph
idx_to_keep = np.logical_not( (xx>=self.window.mx) | (xx<0) | (yy>=self.window.my) | (yy<0))
ValueError: operands could not be broadcast together with shapes (242,) (241,)

Plugin Manager

Good afternoon,

After updating flika to the newest version I have problems installing plugins via the plugin manager. Instead of showing the Install Button, only "Loading Information" is shown in the upper right of the window. Please find the traceback below.

Attempting to install the plugin by copying into the plugins directory does not work either.

Thanks a lot for your help,
best wishes
Ivo

P.S.: Traceback when clicking on any of the plugins in plugin manager.

Exception in thread Thread-1:
Traceback (most recent call last):
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 954, in _bootstrap_inner
self.run()
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 892, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/lib/python3.9/site-packages/flika-0.2.33-py3.9.egg/flika/app/plugin_manager.py", line 249, in loadThread
plug.update_info()
File "/usr/local/lib/python3.9/site-packages/flika-0.2.33-py3.9.egg/flika/app/plugin_manager.py", line 194, in update_info
new_info = parse(txt)
File "/usr/local/lib/python3.9/site-packages/flika-0.2.33-py3.9.egg/flika/app/plugin_manager.py", line 85, in parse
return step(tree)
File "/usr/local/lib/python3.9/site-packages/flika-0.2.33-py3.9.egg/flika/app/plugin_manager.py", line 75, in step
for k in item.getchildren():
Attrib

Pip installed Flika does not support drop events

Not just an issue with the console_scripts entry point for flika, also occurs when running from within the interpreter.

Add a 'subtract black level' feature to the ratio by baseline.

Almost every time someone needs to ratio by baseline, they need to subtract the black level first. It would be convenient to add that feature to the ratio function.

Trace window update

When the file is long and the ROI is big, sometimes the tracefig gets frozen and has to be closed and reopened. It only happens sometimes, it's hard to replicate.

'Plugins' and 'Scripts' Menu don't load in OSX

Error when starting FLIKA - Assertion Error

Hi Kyle,

I'm guessing it is a while since you have been working on FLIKA, so I hope you're still able to get this message. I have been using FLIKA for a while but just recently I got this error on Anaconda prompt which I have never seen before. I've tried uninstalling and reinstalling both flika and anaconda but I still get the same problem. I have no idea where else to go with this as I am not in any way proficient with code, I have just been using FLIKA in the same way in the lab since the start of my PhD!! It would be great if you could take a look.
Many thanks,
Holly

Starting flika
2022-12-05 20:25:55,140 - ERROR - Uncaught exception
Traceback (most recent call last):
File "C:\Users\has54.PHARM\Anaconda3\lib\runpy.py", line 197, in run_module_as_main
return run_code(code, main_globals, None,
File "C:\Users\has54.PHARM\Anaconda3\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\Users\has54.PHARM\Anaconda3\Scripts\flika.exe_main.py", line 7, in
sys.exit(exec())
File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\flika.py", line 123, in exec
fa = start_flika(sys.argv[1:])
File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\flika.py", line 115, in start_flika
fa = FlikaApplication()
File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\app\application.py", line 153, in init
from ..process.file_ import open_file, open_file_from_gui, open_image_sequence_from_gui, open_points, save_file, save_movie_gui, save_points, save_rois
File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\process_init_.py", line 7, in
from .filters import *
File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\process\filters.py", line 89, in
gaussian_blur = Gaussian_blur()
File "C:\Users\has54.PHARM\Anaconda3\lib\site-packages\flika\process\filters.py", line 32, in init
assert 'gaussian' in skimage.filters.dict # Make sure your version of skimage is >= 0.12.3
AssertionError

Plugin Manager UI

When the plugin manager opens, the 'Update', 'Documentation', and 'Download' buttons are present before any plugin is selected. These should be removed.

Also, before any plugin is selected we should have a button that opens a link in a browser that tells you how to submit a new plugin, and a link that goes to a page which has instructions on how to make a plugin. Since we haven't written the pages yet, just point them to a random website and we'll change them later.

tests fail with new tifffile

Make sure flika can open test_images/tubhiswt_C0.ome.tif

BaseProcess preview and Window switch

BaseProcess preview functionality requires that the currentWindow remain the same until accepted or rejected. Some slider ranges are set via g.currentWindow and are only reset on calling gui(). Enable switching the currentWindow to refresh the widgets in the process and reset the image in the old currentWindow.

Unable to install plugins in clean install

I created a fresh flika install in a new python venv using Python 3.11.7 and
flika version 0.3.0 installed from pypi. Once installed, I opened flika by running flika from the command line. I then opened the Plugin Manager and clicked on any of the displayed plugins.

Full stack trace:

2024-02-06 16:41:17,211 - ERROR - Uncaught exception
Traceback (most recent call last):
  File "/Users/kylenv/Desktop/flika_test/flika_py/lib/python3.11/site-packages/flika/app/plugin_manager.py", line 282, in <lambda>
    self.pluginList.currentItemChanged.connect(lambda new, old: self.pluginSelected(new))
                                                                ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/kylenv/Desktop/flika_test/flika_py/lib/python3.11/site-packages/flika/app/plugin_manager.py", line 348, in pluginSelected
    version = parse_version(plugin.version)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/kylenv/Desktop/flika_test/flika_py/lib/python3.11/site-packages/pkg_resources/_vendor/packaging/version.py", line 198, in __init__
    raise InvalidVersion(f"Invalid version: '{version}'")
pkg_resources.extern.packaging.version.InvalidVersion: Invalid version: ''

This bug was first reported in a plugin package here: kyleellefsen/detect_puffs#1

running start_flika() multiple times leads to expanding menus

If you open a command prompt, navigate to flika's directory, start python, and run:

from flika import *
start_flika()
start_flika()

The top level menu items "Image, Process" get added over and over again.

issues with rect_line

• If you try removing the long link from this file, top_line.txt, the link at the opposite side gets deleted.

• If you remove or add a link, the size of one of the light blue circles becomes absolute regardless of the zoom level.

• If you add a link to this ROI, save it, delete the ROI and reopen it from the newly saved file, the new node is linked to the wrong end.

Kymograph of a rectangle ROI

Hi,
Is it possible to get the kymograph from a rectangle selection? I can only get kymograph for a line. It would be nice if the pixels on one side could be averaged and then plot kymograph.

Thanks
Biswajit

Silent plugin errors

If openpyxl is not installed and the puff_detect plugin is being used, when you attempt to save excel files, there is no error displayed anywhere that the dependency is missing. In general, I believe all errors inside plugins are silent.

Plugin Manager crashes

When the Plugin Manager has been open for a few seconds, sometimes Flika crashes with the Windows error: "Python has stopped working." This is possibly related to multithreading?

change 'date' to 'version' in plugin manager in master

ImportError: DLL load failed while importing _rolling_ball_cy: The specified module could not be found.

I receive the error in the title when trying to open flika. Please let me know how I can fix this. I got this error while working on a windows computer but do not get it while working on a mac. I have also attached the full error output in a word document
2021-05-20-Flika-error-2.docx
. Thank you.

Bug installing plugins on Mac

This is the exception I get trying to install a plugin on a Mac.

Butterworth filter

Good afternoon,
When attempting to apply a Butterworth filter to a stack of images, the command seems to get stuck, for the example I ran at "Creating process 14/16". This is not necessarily related to the filter itself, it is accompanied by an error message "Too many open windows". Hitting the "Stop" button leads to IndexError exceptions ("list index out of range") and flika needs to be terminated.

Thanks a lot and best wishes
Ivo

P.S.: Traceback at "Creating process 14/16":

Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/flika-0.2.33-py3.9.egg/flika/process/progress_bar.py", line 28, in run
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 103, in Queue
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/queues.py", line 48, in init
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py", line 68, in Lock
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/synchronize.py", line 162, in init
File "/usr/local/Cellar/[email protected]/3.9.4/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/synchronize.py", line 57, in init
OSError: [Errno 24] Too many open files

Problem with the functions (eg. Subtract/ Ratio)

I am unable to use the the basic functions for some reason on Ipython. - I already did "from flika import *" . Its giving 'ratio' 'subtract' as undefined. I am not sure if I am missing something. Thanks!

Error exporting to external hard drive

On a Mac there is sometimes a problem exporting the data in the trace window to a file on an external drive.

Plugin Manager

The Plugin Manager doesn't detect plugins that were manually placed in the plugins directory.

Permission error saving plugins

We need to change this code from plugin_manager.py:

        try:
            with open("install.zip", "wb") as output:
                output.write(data)

            with zipfile.ZipFile('install.zip', "r") as z:
                folder_name = os.path.dirname(z.namelist()[0])
                z.extractall(get_plugin_directory())

            os.remove("install.zip")

so that 'install.zip' is located outside of flika's directory and the user is guaranteed to have write permissions.

trim down global_vars.py

There are a lot of functions in this file that are no longer used.

checkUpdates() function doesn't work

crashes with:

Traceback (most recent call last):
  File "C:\Users\kyle\Documents\GitHub\flika\flika\global_vars.py", line 199, in checkUpdates
    version = re.findall(r'version=([\d\.]*)', open('flika.py', 'r').read()[:100])
FileNotFoundError: [Errno 2] No such file or directory: 'flika.py'