Multiprocessing

Hi,
I would like to use multiple CPUs for faster analysis, and would like to know how to modify the jupyter notebook script?
Thanks!

"wrong number of arguments" in vectorized call on DataArrays

Hi,

When running the pipeline_noted.ipynb with the demo movies I get the following error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-11-24aa6b1de449> in <module>
      1 hv.output(size=output_size)
      2 if interactive:
----> 3     display(visualize_preprocess(varr_ref.isel(frame=0), denoise, method=['median'], ksize=[5, 7, 9]))

~/Downloads/minian-master/minian/visualization.py in visualize_preprocess(fm, fn, include_org, **kwargs)
   1365         for params in itt.product(*pval):
   1366             fm_res = fn(fm, **dict(zip(pkey, params)))
-> 1367             cur_im, cur_cnt = _vis(fm_res)
   1368             cur_im = cur_im.relabel('After')
   1369             cur_cnt = cur_cnt.relabel('After')

~/Downloads/minian-master/minian/visualization.py in _vis(f)
   1355         im = (hv.Image(f, kdims=['width', 'height'])
   1356                   .opts(**opts_im))
-> 1357         cnt = (hv.operation.contours(im)
   1358                    .opts(**opts_cnt))
   1359         return im, cnt

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/param/parameterized.py in __new__(class_, *args, **params)
   2810         inst = class_.instance()
   2811         inst.param._set_name(class_.__name__)
-> 2812         return inst.__call__(*args,**params)
   2813 
   2814     def __call__(self,*args,**kw):

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/operation.py in __call__(self, element, **kwargs)
    162         elif 'streams' not in kwargs:
    163             kwargs['streams'] = self.p.streams
--> 164         return element.apply(self, **kwargs)
    165 
    166 

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/accessors.py in __call__(self, function, streams, link_inputs, dynamic, **kwargs)
    108             if hasattr(function, 'dynamic'):
    109                 inner_kwargs['dynamic'] = False
--> 110             return function(self._obj, **inner_kwargs)
    111         elif self._obj._deep_indexable:
    112             mapped = []

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/operation.py in __call__(self, element, **kwargs)
    159                                       for k, el in element.items()])
    160             elif isinstance(element, ViewableElement):
--> 161                 return self._apply(element)
    162         elif 'streams' not in kwargs:
    163             kwargs['streams'] = self.p.streams

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/operation.py in _apply(self, element, key)
    119         for hook in self._preprocess_hooks:
    120             kwargs.update(hook(self, element))
--> 121         ret = self._process(element, key)
    122         for hook in self._postprocess_hooks:
    123             ret = hook(self, ret, **kwargs)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/operation/element.py in _process(self, element, key)
    433         xs = element.dimension_values(0, True, flat=False)
    434         ys = element.dimension_values(1, True, flat=False)
--> 435         zs = element.dimension_values(2, flat=False)
    436 
    437         # Ensure that coordinate arrays specify bin centers

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/data/__init__.py in dimension_values(self, dimension, expanded, flat)
    768         """
    769         dim = self.get_dimension(dimension, strict=True)
--> 770         return self.interface.values(self, dim, expanded, flat)
    771 
    772 

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/data/xarray.py in values(cls, dataset, dim, expanded, flat, compute)
    325             da = dask_array_module()
    326             if compute and da and isinstance(data, da.Array):
--> 327                 data = data.compute()
    328             data = cls.canonicalize(dataset, data, data_coords=data_coords,
    329                                     virtual_coords=virtual_coords)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/base.py in compute(self, **kwargs)
    154         dask.base.compute
    155         """
--> 156         (result,) = compute(self, traverse=False, **kwargs)
    157         return result
    158 

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/base.py in compute(*args, **kwargs)
    396     keys = [x.__dask_keys__() for x in collections]
    397     postcomputes = [x.__dask_postcompute__() for x in collections]
--> 398     results = schedule(dsk, keys, **kwargs)
    399     return repack([f(r, *a) for r, (f, a) in zip(results, postcomputes)])
    400 

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/threaded.py in get(dsk, result, cache, num_workers, pool, **kwargs)
     74     results = get_async(pool.apply_async, len(pool._pool), dsk, result,
     75                         cache=cache, get_id=_thread_get_id,
---> 76                         pack_exception=pack_exception, **kwargs)
     77 
     78     # Cleanup pools associated to dead threads

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/local.py in get_async(apply_async, num_workers, dsk, result, cache, get_id, rerun_exceptions_locally, pack_exception, raise_exception, callbacks, dumps, loads, **kwargs)
    460                         _execute_task(task, data)  # Re-execute locally
    461                     else:
--> 462                         raise_exception(exc, tb)
    463                 res, worker_id = loads(res_info)
    464                 state['cache'][key] = res

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/compatibility.py in reraise(exc, tb)
    110         if exc.__traceback__ is not tb:
    111             raise exc.with_traceback(tb)
--> 112         raise exc
    113 
    114     import pickle as cPickle

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/local.py in execute_task(key, task_info, dumps, loads, get_id, pack_exception)
    228     try:
    229         task, data = loads(task_info)
--> 230         result = _execute_task(task, data)
    231         id = get_id()
    232         result = dumps((result, id))

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/core.py in _execute_task(arg, cache, dsk)
    117         func, args = arg[0], arg[1:]
    118         args2 = [_execute_task(a, cache) for a in args]
--> 119         return func(*args2)
    120     elif not ishashable(arg):
    121         return arg

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/optimization.py in __call__(self, *args)
    940                              % (len(self.inkeys), len(args)))
    941         return core.get(self.dsk, self.outkey,
--> 942                         dict(zip(self.inkeys, args)))
    943 
    944     def __reduce__(self):

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/core.py in get(dsk, out, cache)
    147     for key in toposort(dsk):
    148         task = dsk[key]
--> 149         result = _execute_task(task, cache)
    150         cache[key] = result
    151     result = _execute_task(out, cache)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/core.py in _execute_task(arg, cache, dsk)
    117         func, args = arg[0], arg[1:]
    118         args2 = [_execute_task(a, cache) for a in args]
--> 119         return func(*args2)
    120     elif not ishashable(arg):
    121         return arg

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/dask/compatibility.py in apply(func, args, kwargs)
     91     def apply(func, args, kwargs=None):
     92         if kwargs:
---> 93             return func(*args, **kwargs)
     94         else:
     95             return func(*args)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/numpy/lib/function_base.py in __call__(self, *args, **kwargs)
   2089             vargs.extend([kwargs[_n] for _n in names])
   2090 
-> 2091         return self._vectorize_call(func=func, args=vargs)
   2092 
   2093     def _get_ufunc_and_otypes(self, func, args):

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/numpy/lib/function_base.py in _vectorize_call(self, func, args)
   2155         """Vectorized call to `func` over positional `args`."""
   2156         if self.signature is not None:
-> 2157             res = self._vectorize_call_with_signature(func, args)
   2158         elif not args:
   2159             res = func()

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/numpy/lib/function_base.py in _vectorize_call_with_signature(self, func, args)
   2181             raise TypeError('wrong number of positional arguments: '
   2182                             'expected %r, got %r'
-> 2183                             % (len(input_core_dims), len(args)))
   2184         args = tuple(asanyarray(arg) for arg in args)
   2185 

TypeError: wrong number of positional arguments: expected 1, got 2

Could it be a bug due to a new version of dask/numpy like here 'fix a vectorize bug from new dask/numpy version'? Using the docker isn´t working either.
Many thanks in advance!

Error with cross-registration

Hi, I've been working with some of the datasets that I ran through the main pipeline, and I keep running into an error in the visualizing overlapping cells step in the cross-registration notebook.

Unresponsive Kernels during CNMF - dev version

I am having issues when I get to the CNMF step of the pipeline both with the demo and with my own data. When I am running the kernels under "test parameters for spatial update" or "test parameters for temporal update" the kernel gets stuck and never finishes. It will stop at some percentage and the timer will continue to count, but no progress will be made.

It does not occur at the same kernel every time, and when it is able to complete the kernel, it finishes relatively quickly. I have tried letting it run for 48 hours after getting stuck and it never finishes. This has occurred on multiple powerful machines (both windows and mac). I also tried running it on linux through a virtual box within a windows machine, and the same thing happened, although it got further (got stuck on the 2nd temporal update).

I never get an error message, the kernel just becomes unresponsive. Any idea what might be causing this?

I am running on the dev branch as recommended.

Thanks!!

Import Minian Error - no skimage module

Hi--

I love the package overall. I tried sharing the pipeline with lab mates by installing on a few new computers (PCs, Windows 10).

When attempting to install the pipeline for the first time on these new PC's, and verifying the installation using "pipeline_noted" notebook, I receive an error when trying to import the minian modules.

I've included an image of the code and error. Can you please advice how to solve this issue?

Problem with Cross-Registration

I am working with long recording sessions (more than 25 files with 1000 frames) and I have found that minian cannot process them all in one chunk as I face memory errors even when allocating 1.5TB of RAM to the process.
So I have now broken down my session to 3 chunks and have successfully run the pipeline on all and I need to cross-register them now. But unfortunately, I cannot get this notebook to work (I have tried both master and dev branches). The current script on the master branch seems to be functioning with less errors however I still get this error:

My own guess is that the problem comes from when I am opening the datasets:

As you can see, I am opening 3 separate folders of data but apparently, only the last folder has been stored in minian_ds.
I don't set any of the data dimensions manually when I run minian on my videos; Could the problem be because of the naming of the sessions or other data dimensions?
Am I missing something here? Has anyone been able to successfully do a cross-registration on different chunks of a long session?

demo movie origin

Hi @phildong
it will be very helpful if you drop few lines of text about where is your demo movie came from.
I've noticed two things:

The frame size is not the MIniscope's default 752 x 480. Was it resized? If so - what was the resizing method used?
The calcium activity in the movie is very slow comparing to my previous experience. I guess this might be because your recording is from barin area I'm not familiar with. Where is it? Another reason might be that the frame rate is very high (higher that written in the actual file). Another possibility of the slow activity is some bug in my code. Unfortunately I can not open your avi file in my Media Player Classic in order to do code-independent frame rate test - it just crashes. Here is output from my code:
https://ibb.co/yY708kn

Regards,
Denis.

develop / compare cross-registration methods

Better done after last item in #14 . Alternatively, the methods can be bench marked by "exclusivity" and "transitivity" (Ref CellReg). Ideas:

After alignment, either use 2d space of centroids, or run PCA on all A matrices concatenated together and pick principal pixels. Additionally use the low-order G matrix. Then run clustering algorithm on the space composed of spatial and G information.

Adding references in Shifted Target and Template in cross-registration and motion correction

In the alignment part for cross-registration, it will be helpful to add some reference in Shifted Target window as well. Users can easily tell if their alignment works well!
Same idea for visualizing how good the video has been motion corrected after motion correction.

Pre-Batch for individual ROI using in motion correction

    Having a separate pre-batch notebook file for users who wants to select ROI for every video will be helpful! Especially when imaging is not clean which have dirts on either lens or miniscope. Generate an output file for ROI info in each folder, if users don't need to set different ROIs for their videos (don't have that ROI info file in the video folder), can automatically use the default for motion correction.

include an interactive roi draw for motion correction

should be easy to implement with holoviews' box draw stream
http://holoviews.org/gallery/demos/bokeh/box_draw_roi_editor.html

implement metric for motion correction

implement some metric of motion correction. Ideas:

optical flow. Ref: opencv doc, CaImAn implementation

AVStream error & another

Hi,

Recently, from about 1month ago, I start to have a problem making videos(concatenated) with some error message. It seemed like it is ffmpeg related problem, I tried to fix it by downloading ffmpeg again but it did not work, so I want to report it to minian developers. I am using vlc player in Linux ubuntu.

Here I post my error screenshot, with the final product minian.avi file with has white background only (unlike before which used to have 4 divided screens).

And another question: is there any way to change the code in my local computer so that I can generate my final videos after manual curation (delete or merge)? Now it is 'generate video'- 'curation'- then 'save new unit IDs', but these deleted or merged units are not fixed in the video or output display which has been already generated. Could you let me know which part I should change to get them after curation? (Or to plot cells that I am interested in only.)

Thanks!

Image output errors (Hex to RBG)

Hey all!

The pipeline has been working great in terms of data processing, however I have had a significant issue with the visualization necessary to properly define the parameters of the model.
The problem looks like a hex to rgb conversion issue that I've been getting in the denoise and background removal displays. It seems like the function expects to get one value instead of a list, but I am unsure of how to go about fixing this. I have the most recent versions of holoviews, datashader, and panel that are called in the error.

TypeError Traceback (most recent call last)
~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/IPython/core/formatters.py in call(self, obj, include, exclude)
968
969 if method is not None:
--> 970 return method(include=include, exclude=exclude)
971 return None
972 else:

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/dimension.py in repr_mimebundle(self, include, exclude)
1302 combined and returned.
1303 """
-> 1304 return Store.render(self)
1305
1306

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/options.py in render(cls, obj)
1393 data, metadata = {}, {}
1394 for hook in hooks:
-> 1395 ret = hook(obj)
1396 if ret is None:
1397 continue

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/ipython/display_hooks.py in pprint_display(obj)
280 if not ip.display_formatter.formatters['text/plain'].pprint:
281 return None
--> 282 return display(obj, raw_output=True)
283
284

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/ipython/display_hooks.py in display(obj, raw_output, **kwargs)
253 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
254 with option_state(obj):
--> 255 output = layout_display(obj)
256 elif isinstance(obj, (HoloMap, DynamicMap)):
257 with option_state(obj):

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/ipython/display_hooks.py in wrapped(element)
144 try:
145 max_frames = OutputSettings.options['max_frames']
--> 146 mimebundle = fn(element, max_frames=max_frames)
147 if mimebundle is None:
148 return {}, {}

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/ipython/display_hooks.py in layout_display(layout, max_frames)
218 return None
219
--> 220 return render(layout)
221
222

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/ipython/display_hooks.py in render(obj, **kwargs)
66 renderer = renderer.instance(fig='png')
67
---> 68 return renderer.components(obj, **kwargs)
69
70

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/plotting/renderer.py in components(self, obj, fmt, comm, **kwargs)
374 doc = Document()
375 with config.set(embed=embed):
--> 376 model = plot.layout._render_model(doc, comm)
377 if embed:
378 return render_model(model, comm)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/panel/viewable.py in _render_model(self, doc, comm)
415 if comm is None:
416 comm = state._comm_manager.get_server_comm()
--> 417 model = self.get_root(doc, comm)
418
419 if config.embed:

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/panel/viewable.py in get_root(self, doc, comm)
640 """
641 doc = doc or _curdoc()
--> 642 root = self._get_model(doc, comm=comm)
643 self._preprocess(root)
644 ref = root.ref['id']

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/panel/layout.py in _get_model(self, doc, root, parent, comm)
118 if root is None:
119 root = model
--> 120 objects = self._get_objects(model, [], doc, root, comm)
121 props = dict(self._init_properties(), objects=objects)
122 model.update(**self._process_param_change(props))

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/panel/layout.py in _get_objects(self, model, old_objects, doc, root, comm)
108 else:
109 try:
--> 110 child = pane._get_model(doc, root, model, comm)
111 except RerenderError:
112 return self._get_objects(model, current_objects[:i], doc, root, comm)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/panel/pane/holoviews.py in _get_model(self, doc, root, parent, comm)
225 plot = self.object
226 else:
--> 227 plot = self._render(doc, comm, root)
228
229 plot.pane = self

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/panel/pane/holoviews.py in _render(self, doc, comm, root)
284 kwargs = {}
285
--> 286 return renderer.get_plot(self.object, **kwargs)
287
288 def _cleanup(self, root):

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/plotting/bokeh/renderer.py in get_plot(self_or_cls, obj, doc, renderer, **kwargs)
71 combining the bokeh model with another plot.
72 """
---> 73 plot = super(BokehRenderer, self_or_cls).get_plot(obj, doc, renderer, **kwargs)
74 if plot.document is None:
75 plot.document = Document() if self_or_cls.notebook_context else curdoc()

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/plotting/renderer.py in get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
209
210 # Initialize DynamicMaps with first data item
--> 211 initialize_dynamic(obj)
212
213 if not renderer:

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/plotting/util.py in initialize_dynamic(obj)
249 continue
250 if not len(dmap):
--> 251 dmap[dmap._initial_key()]
252
253

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/spaces.py in getitem(self, key)
1278 # Not a cross product and nothing cached so compute element.
1279 if cache is not None: return cache
-> 1280 val = self._execute_callback(*tuple_key)
1281 if data_slice:
1282 val = self._dataslice(val, data_slice)

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/spaces.py in _execute_callback(self, *args)
1052
1053 with dynamicmap_memoization(self.callback, self.streams):
-> 1054 retval = self.callback(*args, **kwargs)
1055 return self._style(retval)
1056

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/core/spaces.py in call(self, *args, **kwargs)
691
692 try:
--> 693 ret = self.callable(*args, **kwargs)
694 except KeyError:
695 # KeyError is caught separately because it is used to signal

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/util/init.py in dynamic_operation(*key, **kwargs)
983
984 def dynamic_operation(*key, **kwargs):
--> 985 key, obj = resolve(key, kwargs)
986 return apply(obj, *key, **kwargs)
987

~/opt/anaconda3/envs/minian/lib/python3.7/site-packages/holoviews/util/init.py in resolve(key, kwargs)
976 elif isinstance(map_obj, DynamicMap) and map_obj._posarg_keys and not key:
977 key = tuple(kwargs[k] for k in map_obj._posarg_keys)
--> 978 return key, map_obj[key]
979
980 def apply(element, *key, **kwargs):