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20.0 20.0 6.0 1.66 MB

General-purpouse camera capture plugin for data streaming to napari

License: MIT License

Python 100.00%

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piapritzke openuc2 felixwanitschke itaykishon-remondo matchboxscope iurillilab

napari-live-recording's Issues

pymmcore-plus: remove startup debug information

At startup of the plugin whenever it tries to discover all possible device adapters available in the Micro-Manager core, it shows the following:

Discovering HID Devices......
HID Device pid: 608d vid: 608d
HID Device pid: 6099 vid: 6099
HID Device pid: 6099 vid: 6099
HID Device pid: 6099 vid: 6099
Discovering USB Devices......

Can this be removed somehow?

Select camera for opencvgraber?

Hi. Is it possible to select camera when using opencvgrabber?
Thanks.
Petro.

Update dependencies

Hi @jacopoabramo,

Working on conda-forge/napari-live-recording-feedstock#4, It seems some dependencies need to be updated

Declared but not used in source code

h5py
np_image_buffer

Could these be updated for the next release?

Cheers!

Processing engine: frame buffer

During live acquisition and recording, each device should be connected to a circular memory buffer on which to store frames acquired at run time. Each device will have it's own independent buffer.
The buffer should be a numpy array which will reflect the current selected ROI for that device. Whenever a new ROI is requested, the content of the frame buffer should be cleared. The size in frames of the buffer will be kept hard-coded and will later connected to a specific UI element.

I am getting error with tifffile library.

Hi.
When I try to start plugin I am getting this error:
ailed to import command at 'napari_live_recording:NapariLiveRecording': cannot import name 'PHOTOMETRIC' from 'tifffile.tifffile' (/home/petro/miniconda3/envs/pyfluoval/lib/python3.9/site-packages/tifffile/tifffile.py)
Any idea what is the problem?

(-2:Unspecified error) The function is not implemented.

Hi Jacapo @jacopoabramo ,

I just tried the new version 0.1.4 of the plugin and it works a little better. I can select a camera and connect to it. However, when I click on ``, the error below pops up.

Is this a bug or is there anything I can do about it?

Thanks!

Best,
Robert

---------------------------------------------------------------------------
error                                     Traceback (most recent call last)
~\AppData\Local\Programs\napari\\app\napari\_qt\qthreading.py in reraise(e=error("OpenCV(4.5.3) C:\\Users\\runneradmin\\App...e or configure script in function 'cvWaitKey'\n"))
    646
    647         def reraise(e):
--> 648             raise e
        e = error("OpenCV(4.5.3) C:\\Users\\runneradmin\\AppData\\Local\\Temp\\pip-req-build-z4706ql7\\opencv\\modules\\highgui\\src\\window.cpp:1340: error: (-2:Unspecified error) The function is not implemented. Rebuild the library with Windows, GTK+ 2.x or Cocoa support. If you are on Ubuntu or Debian, install libgtk2.0-dev and pkg-config, then re-run cmake or configure script in function 'cvWaitKey'\n")
    649
    650         worker.errored.connect(reraise)

~\AppData\Local\Programs\napari\\app\napari\_qt\qthreading.py in run(self=<napari._qt.qthreading.GeneratorWorker object>)
    151                 warnings.filterwarnings("always")
    152                 warnings.showwarning = lambda *w: self.warned.emit(w)
--> 153                 result = self.work()
        result = undefined
        self.work = <bound method GeneratorWorker.work of <napari._qt.qthreading.GeneratorWorker object at 0x00000240537980D0>>
    154             if isinstance(result, Exception):
    155                 if isinstance(result, RuntimeError):

~\AppData\Local\Programs\napari\\app\napari\_qt\qthreading.py in work(self=<napari._qt.qthreading.GeneratorWorker object>)
    365             try:
    366                 input = self._next_value()
--> 367                 output = self._gen.send(input)
        output = undefined
        self._gen.send = <built-in method send of generator object at 0x00000240537D79E0>
        input = None
    368                 self.yielded.emit(output)
    369             except StopIteration as exc:

~\AppData\Local\Programs\napari\python\\Lib\\site-packages\napari_live_recording\_dock_widget.py in yield_acquire_images_forever()
    235             view_time = time()
    236             while True: # infinite loop, quit signal makes it stop
--> 237                 img = self.camera.capture_image()
        img = undefined
        global self.camera.capture_image = undefined
    238                 (self.live_image_buffer.append(img) if img is not None else None)
    239                 new_frame_time = time()

~\AppData\Local\Programs\napari\python\\Lib\\site-packages\napari_live_recording\Cameras\CameraOpenCV.py in capture_image(self=<napari_live_recording.Cameras.CameraOpenCV.CameraOpenCV object>)
     59         _ , img = self.camera.read()
     60         img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
---> 61         cv2.waitKey(1)
        global cv2.waitKey = <built-in function waitKey>
     62         return img
     63

error: OpenCV(4.5.3) C:\Users\runneradmin\AppData\Local\Temp\pip-req-build-z4706ql7\opencv\modules\highgui\src\window.cpp:1340: error: (-2:Unspecified error) The function is not implemented. Rebuild the library with Windows, GTK+ 2.x or Cocoa support. If you are on Ubuntu or Debian, install libgtk2.0-dev and pkg-config, then re-run cmake or configure script in function 'cvWaitKey'

That was my config:

And that's my napari info:

napari: 0.4.11
Platform: Windows-10-10.0.19041-SP0
Python: 3.8.3 (tags/v3.8.3:6f8c832, May 13 2020, 22:37:02) [MSC v.1924 64 bit (AMD64)]
Qt: 5.15.2
PyQt5: 5.15.4
NumPy: 1.19.3
SciPy: 1.7.1
Dask: 2021.08.1
VisPy: 0.8.1

OpenGL:
- GL version: 4.6.14761 Compatibility Profile Context 21.30.02.01 30.0.13002.1001
- MAX_TEXTURE_SIZE: 16384

Screens:
- screen 1: resolution 1920x1200, scale 1.0

Plugins:
- Measurements (Plot profile): 0.1.6
- Measurements (skimage regionprops): 0.1.7
- OtherView: 0.1.1
- Search (Plugin): 0.1.1
- Segment (blobs and things with membranes): 0.2.2
- Segmentation (Accelerated Pixel and Object Classification): 0.5.4
- Segmentation (OCLRFC): 0.4.3
- Segmentation (split/merge): 0.1.3
- StarDist: 2021.6.28
- Utilities (skimage regionprops): 0.1.7
- Visualization(B/C): 0.1.3
- aicsimageio-in-memory: 0.4.1
- aicsimageio-out-of-memory: 0.4.1
- animation: 0.0.2
- cellpose-napari: 0.1.3
- clEsperanto: 0.10.3
- console: 0.0.4
- devbio: 0.1.0
- napari-brushsettings: 0.0.2
- napari-crop: 0.1.0
- napari-czifile2: 0.2.5
- napari-folder-browser: 0.1.2
- napari-itk-io: 0.1.0
- napari-live-recording: 0.1.4
- napari-tabu: 0.1.3
- napari-tools-menu: 0.1.1
- napari_webcam: 0.1.18
- ome-types: 0.2.7
- scikit-image
- stl: 0.0.3
- svg: 0.1.5

Cannot record stacks bigger than 4 GB

Currently there's a limitation in the recording functionality, as stacks bigger than 4 GB (which are considered BigTIFF format according to this) are not properly saved. Recording is handled here:

        @thread_worker(connect={"yielded": add_recording_layer})
        def acquire_stack_images(stack_size: int, file_path: str):

            # todo: move this string replacement at beginning of path acquisition 
            if file_path.endswith(".tiff"):
                file_path.replace(".tiff", ".ome.tiff")

            # todo: should camera acquisition be moved to another thread
            # and yield images to process_stack_images?
            stack = process_stack_images(self.special_function_checkbox.isChecked(), 
                                        np.stack([self.camera.capture_image() for _ in range(0, stack_size)]),
                                        stack_size)

            # todo: stacks bigger than 4 GBs are not saved, how to fix?
            with tifffile.TiffWriter(file_path, append=True) as writer:
                writer.write(stack,
                            photometric="minisblack", 
                            metadata={"axes" : "ZYX"})
            yield file_path

The TiffWriter class has a flag for BigTIFF files, but I tested it and it seems to not be working properly. I would like to make sure that both TIFF and BigTIFF formats are readable from ImageJ in case an user would like to do more post processing operations.

AttributeError when connecting to OpenCV-camera

Hi @jacopoabramo ,

I just tested napari-live-recording again and after clicking on "Connect" to my "Default Camera (OpenCV)", there is an error message popping up:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
~\miniconda3\envs\nap-dev-bio2\lib\site-packages\napari_live_recording\_dock_widget.py in _on_connect_clicked(self=)
    303                 self._set_widgets_enabled(True)
    304                 self.camera_pixel_type_combobox.currentTextChanged.connect(self._on_pixel_format_changed)
--> 305                 self._set_default_roi()
        self._set_default_roi = >
    306             else:
    307                 raise CameraError(f"Error in opening {self.camera.get_name()}")

~\miniconda3\envs\nap-dev-bio2\lib\site-packages\napari_live_recording\_dock_widget.py in _set_default_roi(self=)
    428     def _set_default_roi(self):
    429         self.roi = self.camera.get_sensor_range()
--> 430         self.camera_roi_x_offset_spinbox.setValue(self.roi.offset_x)
        self.camera_roi_x_offset_spinbox.setValue = 
        self.roi.offset_x = undefined
    431         self.camera_roi_y_offset_spinbox.setValue(self.roi.offset_y)
    432         self.camera_roi_x_offset_spinbox.setSingleStep(self.roi.ofs_x_step)

AttributeError: 'NoneType' object has no attribute 'offset_x'

To reproduce: I just started napari, the live recoding plugin, selected the camera and clicked on "Connect".

Afterwards, when I click the start recording button, the plugin works nicely.

Let me know if I can help tracing down that error message.

Happy holidays!

Best,
Robert

Plugin installation fails

Hi Jacopo @jacopoabramo ,

I just installed napari-live-recording in a fresh conda environment and afterwards retrieved the error below from the Plugins > Plugin errors... menu in napari.

I assume, you need to add ximea to the dependencies of the plugin.

Let me know if you need further support in tracing down this issue.

Best,
Robert

==================== Errors for plugin 'napari-live-recording' ====================

napari version: 0.4.12


ERROR #1: Error while importing module napari_live_recording --------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in _load_and_register(self=, mod_name='napari_live_recording', plugin_name='napari-live-recording')
    317         try:
--> 318             module = load(mod_name)
        module = undefined
        global load = 
        mod_name = 'napari_live_recording'
    319             if self.is_registered(module):

~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in load(value='napari_live_recording')
   1041         raise ValueError(f"malformed entry point string: {value}")
-> 1042     module = importlib.import_module(match.group('module'))
        module = undefined
        global importlib.import_module = 
        match.group = 
   1043     attrs = filter(None, (match.group('attr') or '').split('.'))

~\miniconda3\envs\bio_38\lib\importlib\__init__.py in import_module(name='napari_live_recording', package=None)
    126             level += 1
--> 127     return _bootstrap._gcd_import(name[level:], package, level)
        global _bootstrap._gcd_import = 
        name = 'napari_live_recording'
        level = 0
        package = None
    128 

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _gcd_import(name='napari_live_recording', package=None, level=0)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _find_and_load(name='napari_live_recording', import_=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _find_and_load_unlocked(name='napari_live_recording', import_=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _load_unlocked(spec=ModuleSpec(name='napari_live_recording', loader=..._38\\lib\\site-packages\\napari_live_recording']))

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap_external.py in exec_module(self=, module=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _call_with_frames_removed(f=, *args=( at 0x0000014A19CAA920, fil...kages\napari_live_recording\__init__.py", line 1>, {'__builtins__': {'ArithmeticError': , 'AssertionError': , 'AttributeError': , 'BaseException': , 'BlockingIOError': , 'BrokenPipeError': , 'BufferError': , 'BytesWarning': , 'ChildProcessError': , 'ConnectionAbortedError': , ...}, '__cached__': r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-p...ive_recording\__pycache__\__init__.cpython-38.pyc', '__doc__': None, '__file__': r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\__init__.py', '__loader__': , '__name__': 'napari_live_recording', '__package__': 'napari_live_recording', '__path__': [r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording'], '__spec__': ModuleSpec(name='napari_live_recording', loader=..._38\\lib\\site-packages\\napari_live_recording']), '__version__': '0.1.0'}), **kwds={})

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\__init__.py in 
      2 
----> 3 from ._dock_widget import napari_experimental_provide_dock_widget
        global _dock_widget = undefined
        global napari_experimental_provide_dock_widget = undefined

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\_dock_widget.py in 
      5 from imageio import mimwrite, imwrite
----> 6 from napari_live_recording.Cameras import *
        global napari_live_recording.Cameras = undefined
      7 from napari_live_recording.Functions import *

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\Cameras\__init__.py in 
      4 from .CameraOpenCV import *
----> 5 from .CameraXimea import *
        global CameraXimea = undefined
      6 

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\Cameras\CameraXimea.py in 
      4 # see https://www.ximea.com/support/wiki/apis/APIs for more informations
----> 5 from ximea.xiapi import Camera as XiCamera, Xi_error
        global ximea.xiapi = undefined
        global Camera = undefined
        global XiCamera = undefined
        global Xi_error = undefined
      6 from ximea.xiapi import Image as XiImage

ModuleNotFoundError: No module named 'ximea'

The above exception was the direct cause of the following exception:

PluginImportError                         Traceback (most recent call last)
~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in discover(self=, path=None, entry_point=None, prefix=None, ignore_errors=True)
    262 
    263             try:
--> 264                 if self._load_and_register(mod_name, name):
        self._load_and_register = >
        mod_name = 'napari_zelda'
        name = 'napari-zelda'
    265                     count += 1
    266                     self._id_counts[name] = 1

~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in _load_and_register(self=, mod_name='napari_live_recording', plugin_name='napari-live-recording')
    320                 return None
    321         except Exception as exc:
--> 322             raise PluginImportError(
        global PluginImportError = 
        plugin_name = 'napari-live-recording'
        global cause = undefined
        exc = undefined
    323                 f'Error while importing module {mod_name}',
    324                 plugin_name=plugin_name,

PluginImportError: Error while importing module napari_live_recording

ERROR #2: Error while importing module napari_live_recording --------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in _load_and_register(self=, mod_name='napari_live_recording', plugin_name='napari-live-recording')
    317         try:
--> 318             module = load(mod_name)
        module = undefined
        global load = 
        mod_name = 'napari_live_recording'
    319             if self.is_registered(module):

~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in load(value='napari_live_recording')
   1041         raise ValueError(f"malformed entry point string: {value}")
-> 1042     module = importlib.import_module(match.group('module'))
        module = undefined
        global importlib.import_module = 
        match.group = 
   1043     attrs = filter(None, (match.group('attr') or '').split('.'))

~\miniconda3\envs\bio_38\lib\importlib\__init__.py in import_module(name='napari_live_recording', package=None)
    126             level += 1
--> 127     return _bootstrap._gcd_import(name[level:], package, level)
        global _bootstrap._gcd_import = 
        name = 'napari_live_recording'
        level = 0
        package = None
    128 

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _gcd_import(name='napari_live_recording', package=None, level=0)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _find_and_load(name='napari_live_recording', import_=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _find_and_load_unlocked(name='napari_live_recording', import_=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _load_unlocked(spec=ModuleSpec(name='napari_live_recording', loader=..._38\\lib\\site-packages\\napari_live_recording']))

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap_external.py in exec_module(self=, module=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _call_with_frames_removed(f=, *args=( at 0x0000014A19D2D3A0, fil...kages\napari_live_recording\__init__.py", line 1>, {'__builtins__': {'ArithmeticError': , 'AssertionError': , 'AttributeError': , 'BaseException': , 'BlockingIOError': , 'BrokenPipeError': , 'BufferError': , 'BytesWarning': , 'ChildProcessError': , 'ConnectionAbortedError': , ...}, '__cached__': r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-p...ive_recording\__pycache__\__init__.cpython-38.pyc', '__doc__': None, '__file__': r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\__init__.py', '__loader__': , '__name__': 'napari_live_recording', '__package__': 'napari_live_recording', '__path__': [r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording'], '__spec__': ModuleSpec(name='napari_live_recording', loader=..._38\\lib\\site-packages\\napari_live_recording']), '__version__': '0.1.0'}), **kwds={})

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\__init__.py in 
      2 
----> 3 from ._dock_widget import napari_experimental_provide_dock_widget
        global _dock_widget = undefined
        global napari_experimental_provide_dock_widget = undefined

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\_dock_widget.py in 
      5 from imageio import mimwrite, imwrite
----> 6 from napari_live_recording.Cameras import *
        global napari_live_recording.Cameras = undefined
      7 from napari_live_recording.Functions import *

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\Cameras\__init__.py in 
      4 from .CameraOpenCV import *
----> 5 from .CameraXimea import *
        global CameraXimea = undefined
      6 

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\Cameras\CameraXimea.py in 
      4 # see https://www.ximea.com/support/wiki/apis/APIs for more informations
----> 5 from ximea.xiapi import Camera as XiCamera, Xi_error
        global ximea.xiapi = undefined
        global Camera = undefined
        global XiCamera = undefined
        global Xi_error = undefined
      6 from ximea.xiapi import Image as XiImage

ModuleNotFoundError: No module named 'ximea'

The above exception was the direct cause of the following exception:

PluginImportError                         Traceback (most recent call last)
~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in discover(self=, path=None, entry_point=None, prefix=None, ignore_errors=True)
    262 
    263             try:
--> 264                 if self._load_and_register(mod_name, name):
        self._load_and_register = >
        mod_name = 'napari_zelda'
        name = 'napari-zelda'
    265                     count += 1
    266                     self._id_counts[name] = 1

~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in _load_and_register(self=, mod_name='napari_live_recording', plugin_name='napari-live-recording')
    320                 return None
    321         except Exception as exc:
--> 322             raise PluginImportError(
        global PluginImportError = 
        plugin_name = 'napari-live-recording'
        global cause = undefined
        exc = undefined
    323                 f'Error while importing module {mod_name}',
    324                 plugin_name=plugin_name,

PluginImportError: Error while importing module napari_live_recording

ERROR #3: Error while importing module napari_live_recording --------------------

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in _load_and_register(self=, mod_name='napari_live_recording', plugin_name='napari-live-recording')
    317         try:
--> 318             module = load(mod_name)
        module = undefined
        global load = 
        mod_name = 'napari_live_recording'
    319             if self.is_registered(module):

~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in load(value='napari_live_recording')
   1041         raise ValueError(f"malformed entry point string: {value}")
-> 1042     module = importlib.import_module(match.group('module'))
        module = undefined
        global importlib.import_module = 
        match.group = 
   1043     attrs = filter(None, (match.group('attr') or '').split('.'))

~\miniconda3\envs\bio_38\lib\importlib\__init__.py in import_module(name='napari_live_recording', package=None)
    126             level += 1
--> 127     return _bootstrap._gcd_import(name[level:], package, level)
        global _bootstrap._gcd_import = 
        name = 'napari_live_recording'
        level = 0
        package = None
    128 

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _gcd_import(name='napari_live_recording', package=None, level=0)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _find_and_load(name='napari_live_recording', import_=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _find_and_load_unlocked(name='napari_live_recording', import_=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _load_unlocked(spec=ModuleSpec(name='napari_live_recording', loader=..._38\\lib\\site-packages\\napari_live_recording']))

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap_external.py in exec_module(self=, module=)

~\miniconda3\envs\bio_38\lib\importlib\_bootstrap.py in _call_with_frames_removed(f=, *args=( at 0x0000014A19D38870, fil...kages\napari_live_recording\__init__.py", line 1>, {'__builtins__': {'ArithmeticError': , 'AssertionError': , 'AttributeError': , 'BaseException': , 'BlockingIOError': , 'BrokenPipeError': , 'BufferError': , 'BytesWarning': , 'ChildProcessError': , 'ConnectionAbortedError': , ...}, '__cached__': r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-p...ive_recording\__pycache__\__init__.cpython-38.pyc', '__doc__': None, '__file__': r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\__init__.py', '__loader__': , '__name__': 'napari_live_recording', '__package__': 'napari_live_recording', '__path__': [r'C:\Users\rober\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording'], '__spec__': ModuleSpec(name='napari_live_recording', loader=..._38\\lib\\site-packages\\napari_live_recording']), '__version__': '0.1.0'}), **kwds={})

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\__init__.py in 
      2 
----> 3 from ._dock_widget import napari_experimental_provide_dock_widget
        global _dock_widget = undefined
        global napari_experimental_provide_dock_widget = undefined

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\_dock_widget.py in 
      5 from imageio import mimwrite, imwrite
----> 6 from napari_live_recording.Cameras import *
        global napari_live_recording.Cameras = undefined
      7 from napari_live_recording.Functions import *

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\Cameras\__init__.py in 
      4 from .CameraOpenCV import *
----> 5 from .CameraXimea import *
        global CameraXimea = undefined
      6 

~\miniconda3\envs\bio_38\lib\site-packages\napari_live_recording\Cameras\CameraXimea.py in 
      4 # see https://www.ximea.com/support/wiki/apis/APIs for more informations
----> 5 from ximea.xiapi import Camera as XiCamera, Xi_error
        global ximea.xiapi = undefined
        global Camera = undefined
        global XiCamera = undefined
        global Xi_error = undefined
      6 from ximea.xiapi import Image as XiImage

ModuleNotFoundError: No module named 'ximea'

The above exception was the direct cause of the following exception:

PluginImportError                         Traceback (most recent call last)
~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in discover(self=, path=None, entry_point=None, prefix=None, ignore_errors=True)
    262 
    263             try:
--> 264                 if self._load_and_register(mod_name, name):
        self._load_and_register = >
        mod_name = 'napari_zelda'
        name = 'napari-zelda'
    265                     count += 1
    266                     self._id_counts[name] = 1

~\miniconda3\envs\bio_38\lib\site-packages\napari_plugin_engine\manager.py in _load_and_register(self=, mod_name='napari_live_recording', plugin_name='napari-live-recording')
    320                 return None
    321         except Exception as exc:
--> 322             raise PluginImportError(
        global PluginImportError = 
        plugin_name = 'napari-live-recording'
        global cause = undefined
        exc = undefined
    323                 f'Error while importing module {mod_name}',
    324                 plugin_name=plugin_name,

PluginImportError: Error while importing module napari_live_recording
================================================================================

mp4 video saving support

Hi guys!

Great project, I was looking forward for something like this!
I was wondering if you currently have any ongoing/future plan to support writing of mp4 movies.

Thank you in avance for the answer and kudos again!

Dows it work on Windows?

Hello.
Does it work on windows?
Petro.

python-microscope integration

Adding the python-microscope camera device layer to be controlled via the plugin. The guidelines to integrate this layer are as follows:

implementation of the interface described in the file napari_live_recording/control/devices/interface.py
generalized access to all supported python-microscope camera devices and settings
testing the interface using the SimulatedCamera dummy interface provided by the package

Type of tuple is not checked properly

napari-live-recording/src/napari_live_recording/ui/widgets.py

Line 150 in bb061b5

if any(type(param) == float):

An error occurs here, because the type of the tuple is just tuple and is therefore not iterable.

My Solution would be:

if any(isinstance(parameter, float) for parameter in param)

Atribute error prevent import plugin

Wen try to open plugin on fresh environment (Python 3.10.4 Linux, Ubuntu) it crash with:

File ~/Projekty/napari-live-recording/src/napari_live_recording/__init__.py:3
      2 from napari.viewer import Viewer
----> 3 from napari_live_recording.ui import ViewerAnchor
      4 from napari_live_recording.control import MainController

File ~/Projekty/napari-live-recording/src/napari_live_recording/ui/__init__.py:5
      4 from napari_live_recording.common import THIRTY_FPS
----> 5 from napari_live_recording.control.devices import devicesDict, ICamera
      6 from napari_live_recording.control.devices.interface import NumberParameter

File ~/Projekty/napari-live-recording/src/napari_live_recording/control/__init__.py:6
      5 from napari_live_recording.common import FileFormat, ROI
----> 6 from napari_live_recording.control.devices.interface import ICamera
      7 from typing import Dict, NamedTuple

File ~/Projekty/napari-live-recording/src/napari_live_recording/control/devices/__init__.py:13
     10 # iterate through the modules of the devices module
     11 # in order to find all submodules containing the class definitions
     12 # of all cameras
---> 13 for (_, module_name, _) in iter_modules([package_dir]):
        package_dir = PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices')
        [package_dir] = [PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices')]
     14     # import the modulte and iterate through the attributes
     15     try:
     16         # we skip the interface module

File ~/.pyenv/versions/3.10.4/lib/python3.10/pkgutil.py:129, in iter_modules(path=[PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices')], prefix='')
    128 yielded = {}
--> 129 for i in importers:
        importers = <map object at 0x7fb2a0d6b790>
    130     for name, ispkg in iter_importer_modules(i, prefix):

File ~/.pyenv/versions/3.10.4/lib/python3.10/pkgutil.py:421, in get_importer(path_item=PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices'))
    420 try:
--> 421     importer = path_hook(path_item)
        path_item = PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices')
        path_hook = <function FileFinder.path_hook.<locals>.path_hook_for_FileFinder at 0x7fb326360af0>
    422     sys.path_importer_cache.setdefault(path_item, importer)

File <frozen importlib._bootstrap_external>:1632, in path_hook_for_FileFinder(path=PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices'))

File <frozen importlib._bootstrap_external>:1504, in __init__(self=FileFinder(PosixPath('/home/czaki/Projekty/napar...ding/src/napari_live_recording/control/devices')), path=PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices'), *loader_details=((<class '_frozen_importlib_external.ExtensionFileLoader'>, ['.cpython-310-x86_64-linux-gnu.so', '.abi3.so', '.so']), (<class '_frozen_importlib_external.SourceFileLoader'>, ['.py']), (<class '_frozen_importlib_external.SourcelessFileLoader'>, ['.pyc'])))

File <frozen importlib._bootstrap_external>:182, in _path_isabs(path=PosixPath('/home/czaki/Projekty/napari-live-recording/src/napari_live_recording/control/devices'))

AttributeError: 'PosixPath' object has no attribute 'startswith'

To make it work I replaced:

for (_, module_name, _) in iter_modules([package_dir]):

with

for (_, module_name, _) in iter_modules([str(package_dir)]):

in:

File ~/Projekty/napari-live-recording/src/napari_live_recording/control/devices/__init__.py:13

CI failing on Linux with tox

I've been fixing up the CI on GitHub for unit testing. No matter my efforts the CI on ubuntu keeps failing. Some pointers are appreciated.

pymmcore-plus integration

Adding the pymmcore-plus camera device layer to be controlled via the plugin. The guidelines to integrate this layer are as follows:

implementation of the interface described in the file napari_live_recording/control/devices/interface.py
generalized access to all supported pymmcore-plus camera devices and settings
testing the interface using the DemoCamera dummy interface provided by the package

Attribute Error with module

I have this error when i try to activate this plugin

AttributeError                            Traceback (most recent call last)
File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\napari\_qt\menus\plugins_menu.py:105, in PluginsMenu._add_plugin_actions.<locals>._add_toggle_widget(key=('napari-live-recording', 'Live recording'), hook_type='dock')
    102     return
    104 if hook_type == 'dock':
--> 105     self._win.add_plugin_dock_widget(*key)
        key = ('napari-live-recording', 'Live recording')
        self._win = <napari._qt.qt_main_window.Window object at 0x00000161BE726A50>
        self = <napari._qt.menus.plugins_menu.PluginsMenu object at 0x00000161BFD27BE0>
    106 else:
    107     self._win._add_plugin_function_widget(*key)

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\napari\_qt\qt_main_window.py:811, in Window.add_plugin_dock_widget(self=<napari._qt.qt_main_window.Window object>, plugin_name='napari-live-recording', widget_name='Live recording', tabify=False)
    808         wdg = wdg._magic_widget
    809     return dock_widget, wdg
--> 811 wdg = _instantiate_dock_widget(
        Widget = <class 'napari_live_recording.NapariLiveRecording'>
        self = <napari._qt.qt_main_window.Window object at 0x00000161BE726A50>
    812     Widget, cast('Viewer', self._qt_viewer.viewer)
    813 )
    815 # Add dock widget
    816 dock_kwargs.pop('name', None)

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\napari\_qt\qt_main_window.py:1465, in _instantiate_dock_widget(wdg_cls=<class 'napari_live_recording.NapariLiveRecording'>, viewer=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}))
   1460             break
   1461         # cannot look for param.kind == param.VAR_KEYWORD because
   1462         # QWidget allows **kwargs but errs on unknown keyword arguments
   1463 
   1464 # instantiate the widget
-> 1465 return wdg_cls(**kwargs)
        kwargs = {'napari_viewer': Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x00000161B9B79260>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={})}
        wdg_cls = <class 'napari_live_recording.NapariLiveRecording'>

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\napari_live_recording\__init__.py:11, in NapariLiveRecording.__init__(self=<napari_live_recording.NapariLiveRecording object>, napari_viewer=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}))
      9 self.app = QApplication.instance()
     10 self.mainController = MainController()
---> 11 self.anchor = ViewerAnchor(napari_viewer, self.mainController)
        self.mainController = <napari_live_recording.control.MainController object at 0x00000161C8B688B0>
        self = <napari_live_recording.NapariLiveRecording object at 0x00000161C8B47B50>
        napari_viewer = Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x00000161B9B79260>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={})
     12 self.setLayout(self.anchor.mainLayout)
     13 self.app.lastWindowClosed.connect(self.on_close_callback)

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\napari_live_recording\ui\__init__.py:40, in ViewerAnchor.__init__(self=<napari_live_recording.ui.ViewerAnchor object>, napari_viewer=Viewer(camera=Camera(center=(0.0, 0.0, 0.0), zoo...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}), mainController=<napari_live_recording.control.MainController object>)
     38 self.selectionWidget.setDeviceSelectionWidget(list(devicesDict.keys()))
     39 self.selectionWidget.setAvailableCameras(list(devicesDict.keys()))
---> 40 self.recordingWidget = RecordHandling()
        self = <napari_live_recording.ui.ViewerAnchor object at 0x00000161C8B4CC90>
        RecordHandling = <class 'napari_live_recording.ui.widgets.RecordHandling'>
     41 verticalSpacer = QSpacerItem(0, 1, QSizePolicy.Minimum, QSizePolicy.Minimum)
     42 self.mainLayout.addWidget(self.selectionWidget.group)

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\napari_live_recording\ui\widgets.py:397, in RecordHandling.__init__(self=<napari_live_recording.ui.widgets.RecordHandling object>)
    394 self.layout = QGridLayout()
    396 self.formatLabel = QLabel("File format")
--> 397 self.formatComboBox = QEnumComboBox(enum_class=FileFormat)
        self = <napari_live_recording.ui.widgets.RecordHandling object at 0x00000161C8B6A680>
        QEnumComboBox = <class 'superqt.combobox._enum_combobox.QEnumComboBox'>
    398 self.formatLabel.setAlignment(Qt.AlignmentFlag.AlignCenter)
    400 self.folderTextEdit = QLineEdit(
    401     os.path.join(os.path.expanduser("~"), "Documents")
    402 )

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\superqt\combobox\_enum_combobox.py:42, in QEnumComboBox.__init__(self=<superqt.combobox._enum_combobox.QEnumComboBox object>, parent=None, enum_class=<enum 'FileFormat'>, allow_none=False)
     40 self._allow_none = False
     41 if enum_class is not None:
---> 42     self.setEnumClass(enum_class, allow_none)
        self = <superqt.combobox._enum_combobox.QEnumComboBox object at 0x00000161C8B6A8C0>
        enum_class = <enum 'FileFormat'>
        allow_none = False
     43 self.currentIndexChanged.connect(self._emit_signal)

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\superqt\combobox\_enum_combobox.py:53, in QEnumComboBox.setEnumClass(self=<superqt.combobox._enum_combobox.QEnumComboBox object>, enum=<enum 'FileFormat'>, allow_none=False)
     51     super().addItem(NONE_STRING)
     52 names = map(_get_name, self._enum_class.__members__.values())
---> 53 _names = dict.fromkeys(names)  # remove duplicates/aliases, keep order
        names = <map object at 0x00000161D146E560>
     54 super().addItems(list(_names))

File E:\IMAGEJ24\napari_24\.venv\Lib\site-packages\superqt\combobox\_enum_combobox.py:16, in _get_name(enum_value=<FileFormat.ImageJ TIFF: 1>)
     13 def _get_name(enum_value: Enum):
     14     """Create human readable name if user does not implement `__str__`."""
     15     if (
---> 16         enum_value.__str__.__module__ != "enum"
        enum_value = <FileFormat.ImageJ TIFF: 1>
        enum_value.__str__ = <method-wrapper '__repr__' of FileFormat object at 0x00000161C8B4C780>
     17         and not enum_value.__str__.__module__.startswith("shibokensupport")
     18     ):
     19         # check if function was overloaded
     20         name = str(enum_value)
     21     else:

AttributeError: 'method-wrapper' object has no attribute '__module__'```

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