def create_preview(self, file):
image = imaging.load(file)[0]
image = imaging.filters.norm(image, 0.01, 0.01, 0, 255)
# image = imaging.filters.zoom(image, 0.25)
preview_file = '{}.preview.png'.format(file)
imaging.save(image, preview_file)
return preview_file
def topng(mrc, scale, force):
png = pyfs.rext(mrc, 'png')
png = mrc + '.png'
if not force and pyfs.exists(png):
return
print(mrc, '->', png)
image = imaging.load(mrc)[0]
image = imaging.filters.zoom(image, scale)
imaging.save(image, png)
def create_preview(self, file):
try:
image = imaging.load(file)[0]
image = imaging.filters.norm(image, 0.01, 0.01, 0, 255)
image = imaging.filters.zoom(image, 0.25)
preview_file = '{}.preview.png'.format(file)
imaging.save(image, preview_file)
return preview_file
except Exception as e:
print(e)
return None
def test():
path = "cache/13apr24b_00002sq_v02_00004hl_v01_00002en.mrc"
start = 2
stop = 80
levels = 10
ring = 1.2
factor = 0.25
psize = 2
emax = 4.0
vmin = 0.01
image = filters.zoom(load(path), factor)
pyramid = mkpyramid(image, start, stop, levels, ring)
features = find_peaks(pyramid, vmin, emax, psize)
save_pyramid(pyramid, "out")
save(keypoints.draw(image, features[-3000:]), "out.png")
def process_data(self, acquisition_data, motion_correction_data):
if motion_correction_data.dose_weighted_image_file is not None:
aligned_image_file = motion_correction_data.dose_weighted_image_file
else:
aligned_image_file = motion_correction_data.aligned_image_file
output_file_base = os.path.join(self.session.processing_directory, acquisition_data.base_name)
output_file = '{}_dogpicker.json'.format(output_file_base)
try:
image = imaging.load(aligned_image_file)[0]
mint = None
maxt = None
debug = None
meanmax = None
sizemin = int(np.min(motion_correction_data.dimensions)/50)
sizes = np.logspace(np.log10(sizemin), np.log10(sizemin*10) ,num=20)
idogpicker_data = {}
for size in sizes:
keys = list(self.detect(image, size, mint, maxt, debug, meanmax))
LOG.debug("%i -> %i" % (size, len(keys)))
idogpicker_data[int(size+0.5)] = keys
with open(output_file,'w') as fp:
json.dump(pretty_floats(idogpicker_data),fp)
data_model = DogpickerData(acquisition_data.base_name)
data_model.time = time.time()
data_model.dogpicker_file = output_file
data_model.push(self.session.db)
except Exception as e:
LOG.error("Dogpicker failed")
LOG.error(e)
self.failed.append(acquisition_data.base_name)
ResourceManager.release_cpus(self.required_cpus)
return
self.finished.append(acquisition_data.base_name)
ResourceManager.release_cpus(self.required_cpus)
def binby(items, binner):
bins = {}
for item in items:
bin = binner(item)
if bin not in bins:
bins[bin] = []
bins[bin] += [item]
return bins
def save(pyramid, keys, root):
sizes, octave = pyramid[0]
octave = filters.norm(octave, 5, 5, 0, 255)
key_levels = binby(keys, lambda x: int(x.octave))
for l, level in enumerate(octave):
drawn = level
if l in key_levels:
drawn = keypoints.draw(level, key_levels[l])
save(drawn, pyfs.join(root, "%f.png" % sizes[l]), norm=False)
if __name__ == "__main__":
import sys
import imaging
a = imaging.load(
"/Users/craigyk/Desktop/classifier/cache/13apr24b_00002sq_v02_00002hl_v01_00003en.mrc"
)
a = imaging.filters.zoom(a, 0.25)
features = detect(a, start=1.5, levels=5)
save(draw(a, features), sys.argv[1])
def get_dose_from_mrc(self, mrc_path):
imfile = imaging.load(mrc_path)
return (imfile.mean(), imfile.shape[-2::-1])
def preview_montage(self, src, dst, section=0):
image_stack = imaging.load(str(src), format='mrc')
image = image_stack[section]
image = imaging.filters.norm(image, 0.01, 0.01, 0, 255)
imaging.save(image, str(dst), norm=False)
return dst