#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 }