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Extract chooseframe function from segmenter_gui #374

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Jan 10, 2025
Merged

Extract chooseframe function from segmenter_gui #374

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50b56bd
Extract chooseframe function from segmenter_gui
Jan 10, 2025
6048d46
return the image without casting
Jan 10, 2025
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95 changes: 54 additions & 41 deletions ImageD11/nbGui/segmenter_gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,49 @@ def printdatasets( dataroot, sample):
if os.path.isdir( os.path.join( sroot, name ) )
and name.startswith( sample ) ] ) ) )



def chooseframe(self, dset, scan=None, idx=None, counter="_roi1", fetch_raw_image=False):
"""
Locate a busy frame from the dataset and optionally fetch the raw image.

Args:
dset: Dataset object.
scan: Scan to use (default is middle scan).
idx: Frame index (None to auto-detect).
counter: Counter to use for locating the frame.
fetch_raw_image: Whether to fetch the raw image for the frame.

Returns:
scan, idx, raw_image (if fetch_raw_image is True, otherwise None)
"""
if scan is None:
scan = dset.scans[len(dset.scans) // 2]

raw_image = None
with h5py.File(dset.masterfile, "r") as hin:
ctr = dset.detector + counter

if idx is None:
if scan.find("::") > -1: # 1.1::[10000:12000] etc
lo, hi = [int(v) for v in scan[:-1].split("[")[1].split(":")]
scan = scan.split("::")[0]
roi1 = hin[scan]["measurement"][ctr][lo:hi]
idx = np.argmax(roi1) + lo
else: # "1.1"
roi1 = hin[scan]["measurement"][ctr][:]
idx = np.argmax(roi1)

print("Using frame", idx, "from scan", scan)

# placing the raw image
if fetch_raw_image:
raw_image = hin[scan + "/measurement/" + dset.detector][idx]

return scan, idx, raw_image



class SegmenterGui:

""" UI for a jupyter notebook to set the segmentation parameters
Expand All @@ -57,26 +100,11 @@ def __init__(self, dset, counter="_roi1", scan=None, frame=None, cut=1, pixels_i
howmany_slider = widgets.IntSlider(value=np.log10(howmany), min=1, max=15, step=1, description='log(howmany):')
self.widget = widgets.interactive(self.update_image, cut=cut_slider, pixels_in_spot=pixels_in_spot_slider, howmany=howmany_slider)
display( self.widget )

def chooseframe(self, counter):
ds = self.dset
if self.scan is None:
self.scan = ds.scans[len(ds.scans)//2]
if self.idx is not None:
return
# Locate a busy image to look at
with h5py.File(ds.masterfile,'r') as hin:
ctr = ds.detector+counter
if self.scan.find("::") > -1: # 1.1::[10000:12000] etc
lo, hi = [int(v) for v in self.scan[:-1].split("[")[1].split(":")]
self.scan = self.scan.split("::")[0]
roi1 = hin[self.scan]['measurement'][ctr][lo:hi]
self.idx = np.argmax(roi1) + lo
else: # "1.1"
roi1 = hin[self.scan]['measurement'][ctr][:]
self.idx = np.argmax(roi1)
print("Using frame", self.idx, "from scan", self.scan)

# Use the base class method without fetching the raw image
self.scan, self.idx, _ = chooseframe(self.dset, self.scan, self.idx, counter, fetch_raw_image=False)

def segment_frame(self):
"""
ds = ImageD11.sinograms.dataset object
Expand Down Expand Up @@ -137,9 +165,9 @@ def getopts(self):
print("options = ",repr(opts))
return opts


class FrelonSegmenterGui:

""" UI for a jupyter notebook to set the segmentation parameters
From @jadball notebook, @jadball refactored to put in a python file
"""
Expand Down Expand Up @@ -167,27 +195,11 @@ def __init__(self, dset, worker_func, process_func, counter="_roi1", scan=None,
m_offset_thresh=mofft_slider,
m_ratio_thresh=mratt_slider)
display( self.widget )

def chooseframe(self, counter):
ds = self.dset
if self.scan is None:
self.scan = ds.scans[len(ds.scans)//2]
if self.idx is None:
# Locate a busy image to look at
with h5py.File(ds.masterfile,'r') as hin:
ctr = ds.detector+counter
if self.scan.find("::") > -1: # 1.1::[10000:12000] etc
lo, hi = [int(v) for v in self.scan[:-1].split("[")[1].split(":")]
self.scan = self.scan.split("::")[0]
roi1 = hin[self.scan]['measurement'][ctr][lo:hi]
self.idx = np.argmax(roi1) + lo
else: # "1.1"
roi1 = hin[self.scan]['measurement'][ctr][:]
self.idx = np.argmax(roi1)
print("Using frame", self.idx, "from scan", self.scan)
with h5py.File(self.dset.masterfile, 'r') as h5In:
self.raw_image = h5In[self.scan + '/measurement/' + ds.detector][self.idx].astype('uint16')

self.scan, self.idx, self.raw_image = chooseframe(self.dset, self.scan, self.idx, counter, fetch_raw_image=True)
self.raw_image = self.raw_image.astype("uint16")

def segment_frame(self):
image_worker = self.worker_func(**self.options)
goodpeaks = image_worker.peaksearch(img=self.raw_image, omega=0)
Expand Down Expand Up @@ -230,3 +242,4 @@ def getopts(self):
opts = { name: self.options[name] for name in ('bgfile','maskfile','threshold','smoothsigma','bgc','minpx','m_offset_thresh','m_ratio_thresh') }
print("options = ",repr(opts))
return opts