protomo2aligner.py --parallel=True --starting_tlt_file=Manual --r1_region_x=1855 --r2_region_x=1855 --r3_region_x=1855 --r4_region_x=1855 --r5_region_x=1855 --r1_region_y=1919 --r2_region_y=1919 --r3_region_y=1919 --r4_region_y=1919 --r5_region_y=1919 --r1_sampling=8 --r2_sampling=4 --r3_sampling=2 --r4_sampling=1 --r5_sampling=1 --map_sampling=8 --thickness=1500 --r1_mask_width_x=206 --r2_mask_width_x=438 --r3_mask_width_x=902 --r4_mask_width_x=1830 --r5_mask_width_x=1830 --r1_mask_width_y=214 --r2_mask_width_y=454 --r3_mask_width_y=934 --r4_mask_width_y=1894 --r5_mask_width_y=1894 --r1_lowpass_diameter_x=50 --r2_lowpass_diameter_x=25 --r3_lowpass_diameter_x=12.5 --r4_lowpass_diameter_x=6.25 --r5_lowpass_diameter_x=3.125 --r1_lowpass_diameter_y=50 --r2_lowpass_diameter_y=25 --r3_lowpass_diameter_y=12.5 --r4_lowpass_diameter_y=6.25 --r5_lowpass_diameter_y=3.125 --r1_highpass_diameter_x=3270 --r2_highpass_diameter_x=3270 --r3_highpass_diameter_x=3270 --r4_highpass_diameter_x=3270 --r5_highpass_diameter_x=3270 --r1_highpass_diameter_y=3270 --r2_highpass_diameter_y=3270 --r3_highpass_diameter_y=3270 --r4_highpass_diameter_y=3270 --r5_highpass_diameter_y=3270 --r1_mask_apod_x=10 --r2_mask_apod_x=10 --r3_mask_apod_x=10 --r4_mask_apod_x=10 --r5_mask_apod_x=10 --r1_mask_apod_y=10 --r2_mask_apod_y=10 --r3_mask_apod_y=10 --r4_mask_apod_y=10 --r5_mask_apod_y=10 --r1_lowpass_apod_x=125 --r2_lowpass_apod_x=63 --r3_lowpass_apod_x=31 --r4_lowpass_apod_x=16 --r5_lowpass_apod_x=8 --r1_lowpass_apod_y=125 --r2_lowpass_apod_y=63 --r3_lowpass_apod_y=31 --r4_lowpass_apod_y=16 --r5_lowpass_apod_y=8 --r1_highpass_apod_x=1635 --r2_highpass_apod_x=1635 --r3_highpass_apod_x=1635 --r4_highpass_apod_x=1635 --r5_highpass_apod_x=1635 --r1_highpass_apod_y=1635 --r2_highpass_apod_y=1635 --r3_highpass_apod_y=1635 --r4_highpass_apod_y=1635 --r5_highpass_apod_y=1635 --r1_corr_mode=mcf --r2_corr_mode=mcf --r3_corr_mode=mcf --r4_corr_mode=mcf --r5_corr_mode=pcf --r1_iters=14 --r2_iters=10 --r3_iters=5 --r4_iters=10 --r5_iters=0 --preprocessing=true --azimuth_stability_check=False --azimuth_max_deviation=3 --exclude_images_by_angle_accuracy=0.05 --border=100 --clip_low=3.5 --clip_high=3.5 --gradient=true --iter_gradient=false --filter=median --r1_kernel_x=5 --r2_kernel_x=5 --r3_kernel_x=5 --r4_kernel_x=5 --r5_kernel_x=5 --r1_kernel_y=5 --r2_kernel_y=5 --r3_kernel_y=5 --r4_kernel_y=5 --r5_kernel_y=5 --grow=0 --window_area=0.95 --do_estimation=false --norotations=false --correlation_size_x=160 --correlation_size_y=160 --r1_peak_search_radius_x=300 --r2_peak_search_radius_x=300 --r3_peak_search_radius_x=300 --r4_peak_search_radius_x=300 --r5_peak_search_radius_x=300 --r1_peak_search_radius_y=300 --r2_peak_search_radius_y=300 --r3_peak_search_radius_y=300 --r4_peak_search_radius_y=300 --r5_peak_search_radius_y=300 --translimit=959 --orientation=true --azimuth=false --azimuth_switch=8 --elevation=false --rotation=true --scale=false --scale_switch=31 --logging=true --loglevel=2 --create_tilt_video=true --create_reconstruction=true --show_window_size=true --keep_recons=false --slab=true --map_size_x=463 --map_size_y=479 --tilt_clip=true --video_type=html5vid --runname=tiltseries0006 --rundir=/gpfs/appion/jbrasch/17mar17a/protomo_alignments/tiltseries0006 --tiltseries=6 --sessionname=17mar17a --pixelsize=1.76302 --dimx=3710 --dimy=3838 --image_file_type=mrc --coarse=False --projectid=282 --expid=3656 --jobtype=protomo node03 Start time: 2017yr03m27d-23hr40m08s Description: Using Manual alignment for Refinement by copying manual_series0006.tlt to series0006.tlt.Starting Protomo alignment Beginning Refinements Beginning Refinement Iteration #1, Round #1 of Tilt-Series #6 (tiltseries0006) lowpass = 50.0 Angstroms Round #1. Parameters in Protomo units: (Note: At binned by 8, pixelsize is 14.10416 Angstroms, Nyquist is 28.20832 Angstroms) window.lowpass.apodization = { 0.22566656 0.22566656 } map.sampling = 8 window.highpass.diameter = { 0.00862639755352 0.00862639755352 } window.highpass.apodization = { 0.017252795107 0.017252795107 } window.mask.apodization = { 10 10 } align.mask.width = { 206 214 } sampling = 8 align.mask.apodization = { 10 10 } map.body = 150.393377767 map.lowpass.diameter = { 0.5641664 0.5641664 } align.peaksearch.radius = { 300.0 300.0 } window.size = { 231 239 } preprocess.mask.kernel = { 5 5 } window.mask.width = { 206 214 } reference.body = 150.393377767 window.lowpass.diameter = { 0.5641664 0.5641664 } align.correlation.mode = mcf No parameters were switched for Iteration #1 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.04044 for Iteration #1 of Tilt-Series #6. CCMS(rotations) = 0.93007 for Iteration #1 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #1 of Tilt-Series #6. The scaled sum of CCMS values is #0.03882 for Tilt-Series #6. Creating Depiction Videos for Iteration #1 in Parallel... Creating Refinement tilt-series video for iteration #1... Generating Refinement reconstruction for iteration #1... Refinement Iteration #1 finished after retrying 5 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 1536 Window Size (y) was windowed down to 1536 No Round parameters changed for Iteration #2 of Tilt-Series #6 (tiltseries0006) Beginning Refinement Iteration #2, Round #1 of Tilt-Series #6 (tiltseries0006) No parameters were switched for Iteration #2 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (160, 160) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.34712 for Iteration #2 of Tilt-Series #6. CCMS(rotations) = 6.6571 for Iteration #2 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #2 of Tilt-Series #6. The scaled sum of CCMS values is #0.3067 for Tilt-Series #6. Creating Depiction Videos for Iteration #2 in Parallel... Creating Refinement tilt-series video for iteration #2... Generating Refinement reconstruction for iteration #2... Refinement Iteration #2 finished after retrying 39 time(s) due to the sampled search area being too small. Window Size (x) was windowed down to 160 Window Size (y) was windowed down to 160 No Round parameters changed for Iteration #3 of Tilt-Series #6 (tiltseries0006) Beginning Refinement Iteration #3, Round #1 of Tilt-Series #6 (tiltseries0006) No parameters were switched for Iteration #3 Refinement failed. Retry #1 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #2 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #3 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #4 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #5 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #6 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #7 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #8 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #9 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #10 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #11 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #12 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #13 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #14 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #15 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #16 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #17 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #18 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #19 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #20 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #21 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #22 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #23 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #24 with Window Size: (576, 576) (at sampling 8)... Refinement failed. Retry #25 with Window Size: (560, 560) (at sampling 8)... Refinement failed. Retry #26 with Window Size: (512, 512) (at sampling 8)... Refinement failed. Retry #27 with Window Size: (480, 480) (at sampling 8)... Refinement failed. Retry #28 with Window Size: (448, 448) (at sampling 8)... Refinement failed. Retry #29 with Window Size: (432, 432) (at sampling 8)... Refinement failed. Retry #30 with Window Size: (400, 400) (at sampling 8)... Refinement failed. Retry #31 with Window Size: (384, 384) (at sampling 8)... Refinement failed. Retry #32 with Window Size: (336, 336) (at sampling 8)... Refinement failed. Retry #33 with Window Size: (320, 320) (at sampling 8)... Refinement failed. Retry #34 with Window Size: (288, 288) (at sampling 8)... Refinement failed. Retry #35 with Window Size: (256, 256) (at sampling 8)... Refinement failed. Retry #36 with Window Size: (240, 240) (at sampling 8)... Refinement failed. Retry #37 with Window Size: (224, 224) (at sampling 8)... Refinement failed. Retry #38 with Window Size: (192, 192) (at sampling 8)... Refinement failed. Retry #39 with Window Size: (160, 160) (at sampling 8)... Refinement failed. Retry #40 with Window Size: (1728, 1728) (at sampling 8)... Refinement failed. Retry #41 with Window Size: (1680, 1680) (at sampling 8)... Refinement failed. Retry #42 with Window Size: (1600, 1600) (at sampling 8)... Refinement failed. Retry #43 with Window Size: (1568, 1568) (at sampling 8)... Refinement failed. Retry #44 with Window Size: (1536, 1536) (at sampling 8)... Refinement failed. Retry #45 with Window Size: (1440, 1440) (at sampling 8)... Refinement failed. Retry #46 with Window Size: (1344, 1344) (at sampling 8)... Refinement failed. Retry #47 with Window Size: (1296, 1296) (at sampling 8)... Refinement failed. Retry #48 with Window Size: (1280, 1280) (at sampling 8)... Refinement failed. Retry #49 with Window Size: (1200, 1200) (at sampling 8)... Refinement failed. Retry #50 with Window Size: (1152, 1152) (at sampling 8)... Refinement failed. Retry #51 with Window Size: (1120, 1120) (at sampling 8)... Refinement failed. Retry #52 with Window Size: (1024, 1024) (at sampling 8)... Refinement failed. Retry #53 with Window Size: (1008, 1008) (at sampling 8)... Refinement failed. Retry #54 with Window Size: (960, 960) (at sampling 8)... Refinement failed. Retry #55 with Window Size: (896, 896) (at sampling 8)... Refinement failed. Retry #56 with Window Size: (864, 864) (at sampling 8)... Refinement failed. Retry #57 with Window Size: (800, 800) (at sampling 8)... Refinement failed. Retry #58 with Window Size: (784, 784) (at sampling 8)... Refinement failed. Retry #59 with Window Size: (768, 768) (at sampling 8)... Refinement failed. Retry #60 with Window Size: (720, 720) (at sampling 8)... Refinement failed. Retry #61 with Window Size: (672, 672) (at sampling 8)... Refinement failed. Retry #62 with Window Size: (640, 640) (at sampling 8)... Refinement failed. Retry #63 with Window Size: (576, 576) (at sampling 8)... Creating quality assessment statistics... CCMS(shift) = 0.07039 for Iteration #3 of Tilt-Series #6. CCMS(rotations) = 7.1926 for Iteration #3 of Tilt-Series #6. CCMS(scale) = 0.0 for Iteration #3 of Tilt-Series #6. The scaled sum of CCMS values is #0.17905 for Tilt-Series #6. Creating Depiction Videos for Iteration #3 in Parallel... Creating Refinement tilt-series video for iteration #3... Generating Refinement reconstruction for iteration #3...