def dm32h5stack(mrcdir, h5dir):
"""Takes in directory where dm3s containing individual images are and
directory where h5 should go. Stacks all mrcs into one h5 file.
Also returns stacked images and filenames"""
mrcd = mrcdir + '/*.dm3'
filenames = sorted(glob(mrcd))
lenfilename = len(filenames[0])
for f in filenames:
if len(f) != lenfilename:
print(
'changing length of file names indicates that files do not have ordered, decimal numbering'
)
break
d = datetime.datetime.today()
d = d.strftime('%Y%m%d')
h5name = h5dir + '/' + mrcdir.split('/')[-1] + '_' + d + '.h5'
array = []
for idx in np.arange(0, len(filenames), 1):
struct = dm.dmReader(filenames[idx])
data = struct['data']
data = np.expand_dims(data, axis=3)
array.append(data)
array = np.asanyarray(array)
if len(array.shape) == 5:
print('Had to reshape array because its shape is: ', array.shape)
array = array.reshape(array.shape[0], array.shape[2], array.shape[3],
array.shape[4])
i = h5py.File(h5name, 'w')
h5data = i.create_dataset(
'images',
(array.shape[0], array.shape[1], array.shape[2], array.shape[3]),
data=array)
h5data.attrs['files'] = np.array(filenames, dtype='S')
print('Done!')
return (array, filenames)
def save_for_labeller(directory, dm3file):
stack = dm.dmReader(dm3file)
warnings.filterwarnings("ignore")
if os.path.isdir(directory) == False:
os.mkdir(directory)
fname_base = directory + '/' + stack['filename'].split('.')[0]
if len(stack['data'].shape) == 2:
fname = fname_base + '.png'
io.imsave(fname, img)
else:
for idx, img in enumerate(stack['data']):
fname = fname_base + '_' + str(idx) + '.png'
imsave(fname, median_filter(img))
print('done!')
dm4_filepath = 'Capture25.dm4'
# Parameters for dark reference determination
drwidth = 100
# Parameters for electron counting
Nsamples = 40
thresh_bkgrnd_Nsigma = 4
thresh_xray_Nsigma = 30
binfactor = 1
subpixel = False
output = 'pointlist'
# Get memory mapped 4D datacube from dm file
datacube = dm.dmReader(dm4_filepath, dSetNum=0, verbose=False)['data']
datacube = np.moveaxis(datacube, (0, 1), (2, 3))
# Get dark reference
darkreference = 1 # TODO: get_darkreference(datacube = ...!
electron_counted_data = electron_count(
datacube,
darkreference,
Nsamples=Nsamples,
thresh_bkgrnd_Nsigma=thresh_bkgrnd_Nsigma,
thresh_xray_Nsigma=thresh_xray_Nsigma,
binfactor=binfactor,
sub_pixel=True,
output='pointlist')
dm4_filepath = 'Capture25.dm4'
# Parameters for dark reference determination
drwidth = 100
# Parameters for electron counting
Nsamples = 40
thresh_bkgrnd_Nsigma = 4
thresh_xray_Nsigma = 30
binfactor = 1
subpixel = False
output = 'pointlist'
# Get memory mapped 4D datacube from dm file
datacube = dm.dmReader(dm4filename,dSetNum=0,verbose=False)['data']
datacube = np.moveaxis(datacube,(0,1),(2,3))
# Get dark reference
darkreference = 1 # TODO: get_darkreference(datacube = ...!
electron_counted_data = electron_count(datacube, darkreference, Nsamples=Nsamples,
thresh_bkgrnd_Nsigma=thresh_bkgrnd_Nsigma,
thresh_xray_Nsigma=thresh_xray_Nsigma,
binfactor=binfactor,
sub_pixel=True,
output='pointlist')
# For outputting datacubes, wrap counted into a py4DSTEM DataCube
if output=='datacube':
electron_counted_data = DataCube(data=counted)