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Allow user to drop suite2p folder into GUI #837

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Allow user to drop suite2p folder into GUI #837

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2 changes: 2 additions & 0 deletions cellpose/gui/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -946,6 +946,8 @@ def dropEvent(self, event):
files = [u.toLocalFile() for u in event.mimeData().urls()]
if os.path.splitext(files[0])[-1] == '.npy':
io._load_seg(self, filename=files[0])
elif os.path.isdir(files[0]) and os.path.basename(files[0]) == 'suite2p':
io._load_suite2p(self, pathname=files[0])
else:
io._load_image(self, filename=files[0])

Expand Down
90 changes: 83 additions & 7 deletions cellpose/gui/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,61 @@ def _get_train_set(image_names):
train_labels.append(masks)
return train_data, train_labels, train_files


def _load_suite2p_image(parent, pathname=None, image_name='meanImg_chan2'):
# Identify plane folders in suite2p folder
plane_folders = [os.path.basename(p) for p in glob.glob(f"{pathname}/plane*")]
if len(plane_folders)==0:
print(f'GUI_INFO: suite2p folder: {pathname} has no plane folders in it.')
return None

# Identify ops.npy files
ops_files = [glob.glob(f"{pathname}/{plane}/ops.npy") for plane in plane_folders]
if not all([len(ofile)==1 for ofile in ops_files]):
print(f'GUI_INFO: plane folders of {pathname} do not all contain ops.npy files!')
return None

# Get images from ops files
ops = [np.load(ofile[0], allow_pickle=True).item() for ofile in ops_files]
ops_image_shape = [(op['Ly'], op['Lx']) for op in ops]
if not all([image_name in op for op in ops]):
print(f'GUI_INFO: requested image ({image_name}) is not a key of every ops.npy file!')
return None

ops_image = [op[image_name] for op in ops]
if not all([oimage.shape == oimage_shape for oimage, oimage_shape in zip(ops_image, ops_image_shape)]):
print(f'GUI_INFO: requested images ({image_name}) do not all have the expected shape...')
for plane, oimage, oimage_shape in zip(plane_folders, ops_image, ops_image_shape):
print(f' - in {plane}, ops["{image_name}"].shape={oimage.shape} but (ops["Ly"], ops["Lx"])={oimage_shape}')
return None

return ops_image

def _load_suite2p(parent, pathname=None, image_name='meanImg_chan2'):
# attempt to load image from ops.npy files in suite2p folder
ops_image = _load_suite2p_image(parent, pathname=pathname, image_name=image_name)

# Load images into parent
try:
print(f'GUI_INFO: loading {image_name} from every plane in suite2p folder: {pathname}')
image = np.stack(ops_image)
parent.loaded = True
except Exception as e:
print('ERROR: failed to load images, they might have incompatible shapes')
print(f'ERROR: {e}')

# Update GUI
if parent.loaded:
parent.reset()
parent.filename = pathname
parent.filetype = ['suite2p', image_name]
_initialize_images(parent, image, resize=parent.resize, X2=0)
parent.clear_all()
parent.loaded = True
parent.enable_buttons()
# TO DO: Consider integrating loadmasks into this load pipeline if they are already stored?
#if load_mask: _load_masks(parent, filename=mask_file)

def _load_image(parent, filename=None, load_seg=True):
""" load image with filename; if None, open QFileDialog """
if filename is None:
Expand Down Expand Up @@ -129,6 +184,7 @@ def _load_image(parent, filename=None, load_seg=True):
if parent.loaded:
parent.reset()
parent.filename = filename
parent.filetype = 'image'
filename = os.path.split(parent.filename)[-1]
_initialize_images(parent, image, resize=parent.resize, X2=0)
parent.clear_all()
Expand Down Expand Up @@ -239,6 +295,11 @@ def _load_seg(parent, filename=None, image=None, image_file=None):
parent.filename = dat['filename']
if os.path.isfile(parent.filename):
parent.filename = dat['filename']
parent.filetype = dat.get('filetype', 'image')
found_image = True
if os.path.isdir(parent.filename) and dat.get('filetype', 'image')[0] == 'suite2p':
parent.filename = dat['filename']
parent.filetype = dat['filetype']
found_image = True
else:
imgname = os.path.split(parent.filename)[1]
Expand All @@ -247,12 +308,22 @@ def _load_seg(parent, filename=None, image=None, image_file=None):
if os.path.isfile(parent.filename):
found_image = True
if found_image:
try:
image = imread(parent.filename)
except:
parent.loaded = False
found_image = False
print('ERROR: cannot find image file, loading from npy')
if dat.get('filetype', 'image')[0] == 'suite2p':
try:
image_name = dat.get('filetype', ['suite2p', 'meanImg_chan2'])[1]
image = _load_suite2p_image(parent, pathname=parent.filename, image_name=image_name)
image = np.stack(image)
except:
parent.loaded = False
found_image = False
print('ERROR: cannot generate image from suite2p ops.npy files, loading from npy')
else:
try:
image = imread(parent.filename)
except:
parent.loaded = False
found_image = False
print('ERROR: cannot find image file, loading from npy')
if not found_image:
parent.filename = filename[:-11]
if 'img' in dat:
Expand Down Expand Up @@ -488,7 +559,10 @@ def _save_sets(parent):
is forced, e.g. when clicking the save button. Otherwise, use _save_sets_with_check
"""
filename = parent.filename
base = os.path.splitext(filename)[0]
if getattr(parent, 'filetype', 'image')[0] == 'suite2p':
base = os.path.join(filename, 'suite2p')
else:
base = os.path.splitext(filename)[0]
flow_threshold, cellprob_threshold = parent.get_thresholds()
if parent.NZ > 1 and parent.is_stack:
np.save(base + '_seg.npy',
Expand All @@ -497,6 +571,7 @@ def _save_sets(parent):
'masks': parent.cellpix,
'current_channel': (parent.color-2)%5,
'filename': parent.filename,
'filetype': parent.filetype,
'flows': parent.flows,
'zdraw': parent.zdraw,
'model_path': parent.current_model_path if hasattr(parent, 'current_model_path') else 0,
Expand All @@ -511,6 +586,7 @@ def _save_sets(parent):
'chan_choose': [parent.ChannelChoose[0].currentIndex(),
parent.ChannelChoose[1].currentIndex()],
'filename': parent.filename,
'filetype': parent.filetype,
'flows': parent.flows,
'ismanual': parent.ismanual,
'manual_changes': parent.track_changes,
Expand Down