#L0 = 51 # nm 'L104'
#L0 = 76 # nm 'C177'
#L0 = 79 # nm 'O184'
#L0 = 65 # nm 'L176'
#L0 = 128 # nm 'L570'
#L0 = 32 # nm 'SEO30'
#L0 = 30 # nm 'S2VP45'
# layering distance
L0 = 44 # nm 'C67'
q0 = 2 * np.pi / (L0)
# cyl-cyl distance
d_cc = L0 / (np.sqrt(3.0) / 2.0)
process = Protocols.ProcessorIm()
run_args = {
'verbosity': 3,
'local_partition_image_size': 30, # pixels
'local_partition_step': 5.0, # relative to image_size
#'blur' : 1.0, # pixels
'q0': q0, # nm^-1
'dq': q0 * 0.6, # nm^-1
'symmetry': 2,
#'rcParams': {'axes.labelsize': 45,},
'NN_cutoff_distance_nm': L0 * 1.36,
'area_min': L0 * 0.35,
#'area_max' : L0*0.35*20, # Not yet implemented
}
infiles = glob.glob(os.path.join(source_dir, pattern + '.jpg'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'format': 'custom',
'scale': scale, # nm/pixel
'load_param_file': False,
}
run_args = {
'verbosity': 4,
'preprocess': 'custom',
'radius_min': 10, # nm
'radius_max': 50.0, # nm
}
process = Protocols.ProcessorIm(load_args=load_args, run_args=run_args)
#process = Protocols.ProcessorImRGB(load_args=load_args, run_args=run_args)
protocols = [
particles(q0=0.02, threshold=40),
#Protocols.particles_annotated(),
]
# Run
########################################
process.run(infiles, protocols, output_dir=output_dir, force=True)
import glob
#infiles = glob.glob(source_dir + '*.tif')
infiles = glob.glob(source_dir + 'L-36-3cyc_L-74-3-cyc_O2-at-end_1_q01.tif')
#infiles = glob.glob(source_dir + '6.tif')
#infiles = glob.glob(source_dir + '2012-09-25 Lam Blend01-2p5KRPM_q02.tif')
infiles.sort()
if True:
from SciAnalysis.ImAnalysis import Protocols
process = Protocols.ProcessorIm()
#protocols = [ Protocols.thumbnails(crop=1.3) ]
#protocols = [ Protocols.circular_average(ylog=True) ]
#protocols = [ Protocols.thumbnails() ]
load_args = { 'crop_bottom' : 124, # pixels
'scale' : 500.0/353, # nm/pixel
}
run_args = { 'verbosity' : 3,
'local_partition_image_size' : 30, # pixels
'local_partition_step' : 5.0, # relative to image_size
#'blur' : 1.0, # pixels
'q0' : 0.18, # nm^-1
'dq' : 0.18*0.6, # nm^-1
'symmetry' : 4,
L0 = 39.0 # nm 'C67'
q0 = 2 * np.pi / (L0)
# cyl-cyl distance
d_cc = L0 / (np.sqrt(3.0) / 2.0)
#load_args['scale'] = 3000.0/544 # nm/pixel (18k MAG)
#load_args['scale'] = 2000.0/454 # nm/pixel (25k MAG)
#load_args['scale'] = 1000.0/504 # nm/pixel (50k MAG)
#load_args['scale'] = 500.0/302 # nm/pixel (60k MAG)
#load_args['scale'] = 500.0/454 # nm/pixel (90k MAG)
#load_args['scale'] = 500.0/504 # nm/pixel (100k MAG)
#load_args['scale'] = 300.0/454 # nm/pixel (150k MAG)
process = Protocols.ProcessorIm()
run_args = {
'verbosity': 3,
'local_partition_image_size': 30, # pixels
'local_partition_step': 5.0, # relative to image_size
#'blur' : 1.0, # pixels
'q0': q0, # nm^-1
'dq': q0 * 0.6, # nm^-1
'symmetry': 6,
#'rcParams': {'axes.labelsize': 45,},
'NN_cutoff_distance_nm': L0 * 1.36,
'area_min': L0 * 0.35,
'correlation_edge_exclusion': 20,
'correlation_step_size_points': 30,
}
# layering distance
#L0 = 34 # nm 'C67'
L0 = 36 # nm slightly distorted...
#L0 = 40 # nm distorted
q0 = 2 * np.pi / (L0)
#load_args['scale'] = 3000.0/544 # nm/pixel (18k MAG)
#load_args['scale'] = 2000.0/454 # nm/pixel (25k MAG)
#load_args['scale'] = 1000.0/504 # nm/pixel (50k MAG)
#load_args['scale'] = 500.0/302 # nm/pixel (60k MAG)
#load_args['scale'] = 500.0/454 # nm/pixel (90k MAG)
#load_args['scale'] = 500.0/504 # nm/pixel (100k MAG)
#load_args['scale'] = 300.0/454 # nm/pixel (150k MAG)
process = Protocols.ProcessorIm()
run_args = {
'verbosity': 3,
'local_partition_image_size': 30, # pixels
'local_partition_step': 5.0, # relative to image_size
#'blur' : 1.0, # pixels
'q0': q0, # nm^-1
'dq': q0 * 0.6, # nm^-1
'symmetry': 2,
#'rcParams': {'axes.labelsize': 45,},
'NN_cutoff_distance_nm': L0 * 1.36,
'area_min': L0 * 0.35,
'correlation_edge_exclusion': 20,
'correlation_step_size_points': 30,
}
infiles = glob.glob(os.path.join(source_dir, pattern + '.jpg'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'format': 'custom',
'scale': scale, # nm/pixel
'load_param_file': False,
}
run_args = {
'verbosity': 4,
'preprocess': 'custom',
'radius_min': 5, # nm
'radius_max': 100.0, # nm
}
#process = Protocols.ProcessorIm(load_args=load_args, run_args=run_args)
process = Protocols.ProcessorImRGB(load_args=load_args, run_args=run_args)
protocols = [
#particles(q0=0.02, threshold=40),
Protocols.particles_annotated(),
]
# Run
########################################
process.run(infiles, protocols, output_dir=output_dir, force=True)
#L0 = 40 # nm distorted
q0 = 2 * np.pi / (L0)
# cyl-cyl distance
d_cc = L0 / (np.sqrt(3.0) / 2.0)
#load_args['scale'] = 3000.0/544 # nm/pixel (18k MAG)
#load_args['scale'] = 2000.0/454 # nm/pixel (25k MAG)
#load_args['scale'] = 1000.0/504 # nm/pixel (50k MAG)
#load_args['scale'] = 500.0/302 # nm/pixel (60k MAG)
#load_args['scale'] = 500.0/454 # nm/pixel (90k MAG)
#load_args['scale'] = 500.0/504 # nm/pixel (100k MAG)
#load_args['scale'] = 300.0/454 # nm/pixel (150k MAG)
process = Protocols.ProcessorIm()
run_args = {
'verbosity': 3,
'local_partition_image_size': 30, # pixels
'local_partition_step': 5.0, # relative to image_size
#'blur' : 1.0, # pixels
'q0': q0, # nm^-1
'dq': q0 * 0.6, # nm^-1
'symmetry': 2,
#'rcParams': {'axes.labelsize': 45,},
'NN_cutoff_distance_nm': L0 * 1.36,
'area_min': L0 * 0.35,
#'area_max' : L0*0.35*20, # Not yet implemented
}
#L0 = 38.5 # nm 'L75'
#L0 = 76 # nm 'C177'
#L0 = 79 # nm 'O184'
#L0 = 65 # nm 'L176'
#L0 = 128 # nm 'L570'
#L0 = 32 # nm 'SEO30'
#L0 = 30 # nm 'S2VP45'
# layering distance
L0 = 44 # nm 'C67'
q0 = 2 * np.pi / (L0)
# cyl-cyl distance
d_cc = L0 / (np.sqrt(3.0) / 2.0)
process = Protocols.ProcessorIm()
run_args = {
'verbosity': 3,
'q0': q0, # nm^-1
'dq': q0 * 0.6, # nm^-1
'NN_cutoff_distance_nm': L0 * 1.36,
'correlation_step_size_points':
40, # Ignore image edges for grain size analysis
'correlation_edge_exclusion':
50, # Step for grain size analysis (speeds up code)
'radius_min': L0 * 0.08, # nm
'dot_size_cutoff_nm':
L0 * 0.3, # size cutoff for distinguishing a dot vs. line
}