Adding quilt viewer to visualize how FOV is broken up into patches #1156
Conversation
|
Note the natural names for these are patches: in the paper and code we talk about splitting the FOV into patches with stride and overlap. Unfortunately there are already a bunch of patch plotting functions that are for plotting contours of spatial components. Luckily mesmerize had a great name for it: quilt! I have to admit I just recently turned the corner on type hinting because of @pgunn . A couple of notes: I went ahead and used matplotlib/matplotlib#20504 In particular, eventually we'll want to replace For array-like things numpy's |
caiman/utils/visualization.py
Outdated
| col_minmax: array-like | ||
| [col_min, col_max] -- int bounds for rect cols | ||
| color : string | ||
| rectangle color, default 'yellow' |
There was a problem hiding this comment.
Can we stick a link in here indicating what colours are valid?
There was a problem hiding this comment.
Good catch. I shouldn't have specified string there. Any Matplotlib color specification, e.g., rgb tuple or list, or string 'red' is fine (https://matplotlib.org/stable/tutorials/colors/colors.html). I should probably just put Any for this, and be more clear in docs.
| rectangle color, default 'yellow' | ||
| alpha : float | ||
| rectangle alpha (0. to 1., where 1 is opaque), default 0.3 | ||
| ax : pyplot.Axes object |
There was a problem hiding this comment.
Eventually we'll want to add proper typing for this, but no rush
caiman/utils/visualization.py
Outdated
| """ | ||
| Plot patches on template image given stride and overlap parameters. | ||
|
|
||
| Given stride and overlap, plot overlapping patch blocks on template image. |
There was a problem hiding this comment.
Seems to have some redundancy between the 1-sentence and longer description; is this because some tool treats those as separate?
There was a problem hiding this comment.
Yes this is sort of silly. I can just combine them.
caiman/utils/visualization.py
Outdated
| row x col summary image upon which to draw patches (e.g., correlation image) | ||
| stride (int) stride between patches in pixels | ||
| overlap (int) overlap between patches in pixels | ||
| color (str): color of patches, default 'white' |
There was a problem hiding this comment.
probably no need to mention default when it's visible in params.
There was a problem hiding this comment.
This is debated all over the place. I've noticed in our code we have it in both places, so I've done this too. But it is a maintenance headache and is asking for trouble/inconsistencyes. Happy to stop doing it moving forward.
There was a problem hiding this comment.
It's not really a big deal either way, it's just another thing to maintain if it changes in one place.
caiman/utils/visualization.py
Outdated
| alpha: Optional[float]=0.3, | ||
| vmin: Optional[float]=0.0, | ||
| vmax: Optional[float]=0.6, | ||
| figsize: Optional[Tuple]=(6,6)) -> Any: |
There was a problem hiding this comment.
Is this Optional[Tuple[float,float]] or Optional[Tuple[int,int]]?
The default seems to disagree with the comment section
There was a problem hiding this comment.
Good catch, fixing (it's float,float)
caiman/utils/visualization.py
Outdated
| axes object upon which rectangle will be drawn, default None | ||
|
|
||
| Returns: | ||
| ax (Axes object) |
There was a problem hiding this comment.
If we don't want to specify types for these, can we say a little bit more about what we expect them to be? matplotlib.axes?
caiman/utils/visualization.py
Outdated
| ax (Axes object) | ||
| rect (Rectangle object) | ||
| """ | ||
| from matplotlib.patches import Rectangle |
There was a problem hiding this comment.
Imports don't go in methods/functions; please move this to the head of the file
Description
Adds functionality to visualize overlapping patches that split up field of view for motion correction and cnmf for parellelization. Useful when picking different spatial parameters (
rf/stride/gSig/gSizfor 8000 cnmf, andstrides/overlapsfor motion correction).Thanks to @kushalkolar (mesmerize) for idea of
quiltname, aspatchesis already used for viewing spatial contours.Fixes #1116
Type of change
Has your PR been tested?
I ran the tests there are no new errors introduced in dev branch. I have tested the plotting functionality fairly extensively, have not yet added new tests to
caiman/tests