io.masks_flows_to_seg is not working anymore when setting the diameter by hand

[rmathieu25]

Hello!

Thank you for developing Cellpose. I used it for almost one year now and it is great!

Since your last update, I have an issue when running the io.masks_flows_to_seg. It is working only if the diameter is set to None. If I set the diameter by hand, I get the following issue (I am running Cellpose with colab):

from cellpose import io
io.masks_flows_to_seg(imgs,masks, flows, diams, files, channels)
---------------------------------------------------------------------------

TypeError                                 Traceback (most recent call last)

<ipython-input-31-7605babb8af9> in <module>()
      1 from cellpose import io
      2 
----> 3 io.masks_flows_to_seg(imgs,masks, flows, diams, files, channels)

/usr/local/lib/python3.7/dist-packages/cellpose/io.py in masks_flows_to_seg(images, masks, flows, diams, file_names, channels)
    216 
    217     if isinstance(masks, list):
--> 218         for k, [image, mask, flow, diam, file_name] in enumerate(zip(images, masks, flows, diams, file_names)):
    219             channels_img = channels
    220             if channels_img is not None and len(channels) > 2:

TypeError: zip argument #4 must support iteration

[rmathieu25]

I am sorry but I am still running into the same error despite your commit

[carsen-stringer]

you're running the github version? can you give me more info about your error please? It should make diameters a list if masks is a list

[rmathieu25]

Hello!

Yes I'm running the github version. The error occurred only if I set a single number for all images for the diameter argument.
for example:

channels = [[1,0]] 
masks, flows, styles, diams = model.eval(imgs, diameter=20, flow_threshold=None,channels=channels, cellprob_threshold=-2)

But giving a list solved the error. By running:

channels = [[1,0]] 

diameter=[20]*nimg
masks, flows, styles, diams = model.eval(imgs, diameter=diameter, flow_threshold=None,channels=channels, cellprob_threshold=-2)

I don't get the error

[carsen-stringer]

are you sure you are using the latest version of the code?

channels = [[2,3]]
imgs = [io.imread(filename) for filename in files]
masks, flows, styles, diams = model.eval(imgs, diameter=30, channels=channels)
io.masks_flows_to_seg(imgs, masks, flows, diams, files, channels)
io.save_to_png(imgs, masks, flows, files)

the above does not error for me

[carsen-stringer]

also

io.masks_flows_to_seg(imgs, masks, flows, 30, files, channels)

does not error

[rmathieu25]

Hello!

I haven't changed anything since yesterday but it is working now...

Thank you very much

[carsen-stringer]

hurray!