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man_adjust.py
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''' Dictionaries of image parameters in the strict format:
Filename: (image threshold), (image crop), (Estimated NP diameter)
Examples:
Fiber1:(140,255),(1200,3000,400,4000),(30)
Fiber2: (122,255), (None),(None)
Store builtin sizes here. All folder names MUST BE TRUE to the
name of directory of datain
'''
old_30 = 30.0 #nm
old_16 = 16.0 #nm
pella_50 = 48.6 #nm
new_22 = 22.0 #nm
new_18 = 18.0 #nm
manual_adjustments = {}
manual_adjustments['aug_6_12'] = { #/2012/August/8_4_6_First_SEM_Experiment/8_6_MIDSIZED_BY_MAG AND 8_6_SMALLNPS_BY_MAG
'8_b1_f2_100k2_low.tif':((138 ,255), (23, 13, 998, 585),(old_30)),
'8_b1_f2_100k2_high.tif':((164 ,255), (23, 13, 998, 586),(old_30)),
'8_b1_f2_80k2_low.tif':((116 ,255), (14, 80, 996, 516),(old_30)),
'8_b1_f2_80k2_high.tif':((149 ,255), (14, 80, 996, 517),(old_30)),
'8_b1_f2_50k3_low.tif':((131 ,255), (5, 15, 1013, 583),(old_30)),
'8_b1_f2_50k3_high.tif':((142 ,255), (5, 15, 1013, 584),(old_30)),
'8_b1_f2_30k2_low.tif':((139 ,255), (11, 13, 922, 566),(old_30)),
'8_b1_f2_30k2_high.tif':((165 ,255), (11, 13, 922, 567),(old_30)),
'8_b1_f4_50k5_low.tif':((144 ,255), (5, 6, 1002, 550),(old_30)),
'8_b1_f4_50k5_high.tif':((182 ,255), (5, 6, 1002, 551),(old_30)),
'8_b1_f4_30k3_low.tif':((137 ,255), (4, 4, 1014, 589),(old_30)),
'8_b1_f4_30k3_high.tif':((168 ,255), (4, 4, 1014, 590),(old_30)),
'8_b2_f2_100k2_low.tif':((157 ,255), (7, 211, 650, 455),(old_30)),
'8_b2_f2_100k2_high.tif':((169 ,255), (7, 211, 650, 456),(old_30)),
'8_b2_f2_80k_low.tif':((144 ,255), (20, 252, 650, 363),(old_30)),
'8_b2_f2_80k_high.tif':((154 ,255), (20, 252, 650, 363),(old_30)),
'8_b2_f2_50k2_low.tif':((159 ,255), (114, 6, 906, 588),(old_30)),
'8_b2_f2_50k2_high.tif':((173 ,255), (114, 6, 906, 589),(old_30)),
'8_b2_f3_100k2_low.tif':((112 ,255), (3, 11, 1017, 591),(old_30)),
'8_b2_f3_100k2_high.tif':((122 ,255), (3, 11, 1017, 592),(old_30)),
'8_b2_f3_50k3_low.tif':((144 ,255), (104, 2, 816, 598),(old_30)),
'8_b2_f3_50k3_high.tif':((155 ,255), (104, 2, 816, 599),(old_30)),
'8_b2_f3_30k_low.tif':((140 ,255), (275, 4, 746, 599),(old_30)),
'8_b2_f3_30k_high.tif':((160 ,255), (275, 4, 746, 600),(old_30)),
'8_b2_f3_30k3_low.tif':((147 ,255), (3, 4, 541, 661),(old_30)),
'8_b2_f3_30k3_high.tif':((150 ,255), (3, 4, 541, 662),(old_30)),
'8_b3_f3_50k3_low.tif':((122 ,255), (20, 205, 985, 379),(old_30)),
'8_b3_f3_50k3_high.tif':((136 ,255), (20, 205, 985, 380),(old_30)),
'8_b3_f3_30k_low.tif':((128 ,255), (186, 91, 578, 457),(old_30)),
'8_b3_f3_30k_high.tif':((141 ,255), (186, 91, 578, 458),(old_30)),
'8_b3_f4_100k3_low.tif':((136 ,255), (2, 11, 1016, 590),(old_30)),
'8_b3_f4_100k3_high.tif':((155 ,255), (2, 11, 1016, 590),(old_30)),
'8_b3_f4_50k2_low.tif':((155 ,255), (38, 39, 335, 630),(old_30)),
'8_b3_f4_50k2_high.tif':((163 ,255), (38, 39, 335, 631),(old_30)),
'8_b3_f4_30k3_low.tif':((157 ,255), (9, 138, 488, 533),(old_30)),
'8_b3_f4_30k3_high.tif':((161 ,255), (9, 138, 488, 533),(old_30)),
'8_b1_f3_100k_low.tif':((131 ,255), (2, 3, 1019, 597),(old_30)),
'8_b1_f3_100k_high.tif':((141 ,255), (2, 3, 1019, 597),(old_30))
}
manual_adjustments['aug_13_12'] = { #2012/August/8_13_Second_SEM_Experiment/8_13_BYMAG_FOR_SEMANALYSIS
'f1_b1_15k21_low.tif':((143, 255),(1, 0, 1023, 628),(old_30)),
'f1_b1_15k21_high.tif':((147, 255),(1, 0, 1023, 628),(old_30)),
'f1_b1_30k2kx1_low.tif':((150, 255),(2, 1, 1020, 625),(old_30)),
'f1_b1_30k2kx1_high.tif':((157, 255),(2, 1, 1020, 625),(old_30)),
'f1_b1_30k1kx1_low.tif':((133, 255),(3, 30, 1021, 630),(old_30)),
'f1_b1_30k1kx1_high.tif':((122, 255),(3, 30, 1021, 630),(old_30)),
'f1_b1_50kx31_low.tif':((120, 255),(0, 2, 625, 672),(old_30)),
'f1_b1_50kx31_high.tif':((133, 255),(0, 2, 625, 672),(old_30)),
'f1_b1_100k11_low.tif': ((138, 255),(1, 33, 1017, 549),(old_30)),
'f1_b1_100k11_high.tif': ((144, 255),(1, 33, 1017, 549),(old_30)),
'f2_b1_5K21_low.tif': ((95, 255),(2, 1, 727, 536),(old_30)), #5k not 50k
'f2_b1_5K21_high.tif': ((108, 255),(2, 1, 727, 536),(old_30)),
'f2_b1_15k_highres_9scan_11int1_low.tif': ((96, 255),(2, 2, 1020, 631),(old_30)),
'f2_b1_15k_highres_9scan_11int1_high.tif': ((103, 255),(2, 2, 1020, 631),(old_30)),
'f2_b1_30k31_low.tif': ((112, 255),(2, 14, 1020, 619),(old_30)),
'f2_b1_30k31_high.tif': ((120, 255),(2, 14, 1020, 619),(old_30)),
'f2_b1_50k21_low.tif': ((119, 255),(6, 9, 1007, 625),(old_30)),
'f2_b1_50k21_high.tif': ((121, 255),(6, 9, 1007, 625),(old_30)),
'f2_b1_100k21_low.tif':((112, 255),(5, 18, 1012, 614),(old_30)),
'f2_b1_100k21_high.tif':((145, 255),(5, 18, 1012, 614),(old_30)),
'f1_b2_5k21_low.tif':((129, 255),(4, 3, 434, 556),(old_30)),
'f1_b2_5k21_high.tif':((133, 255),(4, 3, 434, 556),(old_30)),
'f1_b2_15k11_low.tif':((95, 255),(4, 24, 1012, 604),(old_30)),
'f1_b2_15k11_high.tif':((128, 255),(4, 24, 1012, 604),(old_30)),
'f1_b2_30k21_low.tif':((130, 255),(5, 25, 989, 600),(old_30)),
'f1_b2_30k21_high.tif':((140, 255),(5, 25, 989, 600),(old_30)),
'f1_b2_50k11_low.tif':((110, 255),(14, 25, 984, 604),(old_30)),
'f1_b2_50k11_high.tif':((130, 255),(14, 25, 984, 604),(old_30)),
'f1_b2_100k11_low.tif':((103, 255),(49, 64, 916, 568),(old_30)),
'f1_b2_100k11_high.tif':((128, 255),(49, 64, 916, 568),(old_30)),
'f1_b2_100k21_low.tif':((115, 255),(24, 152, 966, 314),(old_30)), #Added by adam later, (alread added to spreadsheet)
'f1_b2_100k21_high.tif':((157, 255),(24, 152, 966, 314),(old_30)),
'f2_b2_5k21_low.tif':((107, 255),(637, 284, 371, 342),(old_30)),
'f2_b2_5k21_high.tif':((129, 255),(637, 284, 371, 342),(old_30)),
'f2_b2_15k31_low.tif':((107, 255),(20, 50, 788, 612),(old_30)),
'f2_b2_15k31_high.tif':((126, 255),(20, 50, 788, 612),(old_30)),
'f2_b2_30k31_low.tif':((92, 255),(6, 18, 1004, 606),(old_30)),
'f2_b2_30k31_high.tif':((149, 255),(6, 18, 1004, 606),(old_30)),
'f2_b2_50k31_low.tif':((100, 255),(13, 32, 967, 598),(old_30)),
'f2_b2_50k31_high.tif':((138, 255),(13, 32, 967, 598),(old_30),)
}
### Note: All of these are low res images and were performed by Annie.
#Careful, this has some odd/mixed up filenames. Fix these on ones that you intend to use.
manual_adjustments['aug_22_12'] = {
'f1_50000_low.tif':((101,255),(3,3,3063,1971),(old_30)),
'f1_50000_high.tif':((120,255),(3,3,3063,1971),(old_30)),
'f1_30500.tif':((121,255),(30, 30, 3030, 1872),(old_30)),
'f2_30000.tif':((99,255), (30,30,3030,1872), (old_30)),
'f3_50k_low_res_7_11_low.tif':((95,255),(0,0,1023,738),(old_30)),
'f4_30000_1.tif':((150,255), (4,5,1020,721), (old_30))
}
manual_adjustments['sept_5_12'] = { #THERE ARE WAY MORE IMAGES THAN JUST THESE ONES
######F1
#'f1_5000.tif':( (163, 255),(1533, 9, 1422, 1104),(old_30)), #No aggregates in crop
'f1_5000.tif':( (163, 255),(1242, 9, 1713, 1053),(old_30)), #Huge aggregate in crop
'f1_10000.tif':( (166, 255),(None),(old_30)),
'f1_15000.tif':( (172, 255),(None),(old_30)),
#'f1_30000.tif': ( (158, 255), (None),(old_30)),
'f1_30000_low.tif': ( (155, 255), (None),(old_30)),
'f1_30000_high.tif': ( (183, 255), (None),(old_30)),
#######F2
'f2_5000.tif':( (152, 255), (951, 36, 1581, 2145),(old_30)),
'f2_10000.tif':( (157, 255), (None),(old_30)),
# 'f2_14390.tif':( (164, 255), (None),(old_30)),
'f2_14390.tif':( (157, 255), (None),(old_30)), #Trying to be identical with figures above
# 'f2_30000.tif':( (144, 255), (None),(old_30)),
'f2_30000_low.tif':( (145, 255), (None),(old_30)),
'f2_30000_high.tif':( (164, 255), (None),(old_30)),
### F2 LOW HIGH ESTIMATION (added 12/19/12)
'f2_5000_low.tif':( (148, 255), (951, 36, 1581, 2145),(old_30)),
'f2_5000_high.tif':( (166, 255), (951, 36, 1581, 2145),(old_30)),
'f2_10000_low.tif':( (153, 255), (None),(old_30)),
'f2_10000_high.tif':( (174, 255), (None),(old_30)),
'f2_14390_low.tif':( (144, 255), (None),(old_30)), #Trying to be identical with figures above
'f2_14390_high.tif':( (174, 255), (None),(old_30)), #Trying to be identical with figures above
#######F3
'f3_5000.tif':( (144,255), (None),(old_30)),
'f3_9490.tif':((148,255),(None),(old_30)),
'f3_10000.tif':( (174,255), (42,144,2997,2109),(old_30)),
'f3_15000.tif':( (125,255), (None),(old_30)),
'f3_30000.tif':( (128, 255), (None),(old_30)),
#######F4 (very high saturation, individual particles tough to distinguish)
####### Therefore, to get accurate coverage, need a high threshold estimate, to get particle distribution, less threshold
'f4_5000.tif':((110,255),(597, 18, 2466, 2265),(old_30)),
'f4_5000_low.tif':((108,255),(597, 18, 2466, 2265),(old_30)),
'f4_5000_high.tif':((153,255),(597, 18, 2466, 2265),(old_30)),
#'f4_10000_scan7_int11.tif':((129, 255),(0, 1059, 1680, 1242),(old_30)),
'f4_10000_scan7_int11.tif':((127, 255),(9, 9, 3057, 924),(old_30)), #Additional crop
'f4_10000_scan7_int11_low.tif':((98, 255),(9, 9, 3057, 924),(old_30)),
'f4_10000_scan7_int11_high.tif':((110, 255),(9, 9, 3057, 924),(old_30)),
'f4_10000_scan9.tif':((126,255),(60, 870, 2997, 1413),(old_30)),
'f4_15000_scan91.tif':((129,255),(60, 465, 2976, 1976),(old_30)),
'f4_15000_scan91_low.tif':((100,255),(60, 465, 2976, 1976),(old_30)),
'f4_15000_scan91_high.tif':((149,255),(60, 465, 2976, 1976),(old_30)),
'f4_30000_scan7_int111_low.tif':((87,255),(15, 273, 3042, 1986),(old_30)), #Low Thresh, individual particles more distinct!!!
'f4_30000_scan7_int111_high.tif':((128,255),(15, 273, 3042, 1986),(old_30)), #High Thresh, individual coverage more accurate!!!
'f4_30000_scan7_int111_low_nocrop.tif':((88,255),(None),(old_30)), #Low Thresh, individual particles more distinct!!!
'f4_50000_scan7_int111_high.tif':((143, 255),(6, 129, 3066, 2157),(old_30)), #LOW Thresh, individual particles more distinct!!!
'f4_50000_scan7_int111_low.tif':((98, 255),(6, 129, 3066, 2157),(old_30)), #HIGH thresh, coverage more accurate
}
### Performed by Annie
manual_adjustments['oct_23_12'] = {
'fiber1_50000_low.tif':((97, 255),(None),(pella_50)),
'fiber1_50000_high.tif':((117, 255),(None),(pella_50)),
'fiber1_30000_low.tif':((103, 255),(None),(pella_50)),
'fiber1_30000_high.tif':((115, 255),(None),(pella_50)),
'fiber1_10000_low.tif':((88, 255),(None),(pella_50)),
'fiber1_10000_high.tif':((115, 255),(None),(pella_50)),
'fiber2_50000_low.tif':((93, 255),(141, 258, 2616, 1947),(pella_50)),
'fiber2_50000_high.tif':((128, 255),(141, 258, 2616, 1947),(pella_50)),
'fiber2_30000_low.tif':((114, 255),(6, 864, 3054, 1434),(pella_50)),
'fiber2_30000_high.tif':((136, 255),(6, 864, 3054, 1434),(pella_50)),
'fiber2_10000_low.tif':((120, 225),(1056, 3, 2010, 2295),(pella_50)),
'fiber2_10000_high.tif':((134, 225),(1056, 3, 2010, 2295),(pella_50)),
### Performed by Zhaowen
'fiber3_30000_scan6_line113_low.tif':((116, 255),(6, 999, 3048, 1302),(pella_50)),
'fiber3_30000_scan6_line113_high.tif':((135, 255),(6, 999, 3048, 1302),(pella_50)),
'fiber3_50000_low.tif':((136, 255),(None),(pella_50)),
'fiber3_50000_high.tif':((145, 255),(None),(pella_50)),
'fiber3_50000_2_low.tif':((125, 255),(None),(pella_50)),
'fiber3_50000_2_high.tif':((143, 255),(None),(pella_50)),
'fiber3_100000_low.tif':((119, 255),(9, 897, 3054, 1371),(pella_50)),
'fiber3_100000_high.tif':((143, 255),(9, 897, 3054, 1371),(pella_50)),
'fiber4_10000_low.tif':((105, 255),(21, 15, 3018, 1344),(pella_50)),
'fiber4_10000_high.tif':((120, 255),(21, 15, 3018, 1344),(pella_50)),
'fiber4_30000_low.tif':((100, 255),( 21, 972, 3051, 1320),(pella_50)),
'fiber4_30000_high.tif':((122, 255),(21, 972, 3051, 1320),(pella_50)),
'fiber4_50000_low.tif':((100, 255),( 15, 12, 3042, 1572),(pella_50)),
'fiber4_50000_high.tif':((115, 255),(15, 12, 3042, 1572),(pella_50)),
'fiber4_100000_2_low.tif':((102, 255),(9, 9, 2589, 2283),(pella_50)),
'fiber4_100000_2_high.tif':((112, 255),(9, 9, 2589, 2283),(pella_50),)
}
### If I get lazy and want to rename a file on the fly to mix between runs, I just put it here.
manual_adjustments['special_renames'] = { #IS THIS FROM OCT 23? TED PELLA?
'f3_100000_low.tif':((112 ,255), (3, 11, 1017, 591),()),
'f3_100000_high.tif':((122 ,255), (3, 11, 1017, 592))
}
### RENAME THESE WITH UNDERSCORE OR THEY WONT SORT CORRECTLY!!!
manual_adjustments['june_TEM']={
'5C-1-60k-16b.tif':( (0, 18247),(None),()), '5C-2-60k-16b.tif':( (),(None) )
}
manual_adjustments['jan_15_13'] = {
'f1_10000_2_low.tif':((46,255),(6,6,3054,2052),(pella_50)),
'f1_10000_2_high.tif':((50,255),(6,6,3054,2052),(pella_50)),
'f1_30000_low.tif':((64,255),(12,12,3051,2049),(pella_50)),
'f2_10000_low.tif':((70,255),(9,12,3051,2046),(pella_50)),
'f2_10000_high.tif':((76,255),(9,12,3051,2046),(pella_50)),
'f2_30000_low.tif':((67,255),(6,9,2967,2046),(pella_50)),
'f2_30000_high.tif':((72,255),(6,9,2967,2046),(pella_50)),
'f2_30000_2.tif':((77,255),(9, 15, 3063, 2016),(pella_50)),
'f2_30000_3.tif':((75,255),(9, 19, 3063, 2030),(pella_50)),
###the 10k image is extremely dark; check how resulting estimate compares to other 10k images.
'f3_10000_low.tif':((29,255),(6,6,3054,2061),(pella_50)),
'f3_10000_high.tif':((32,255),(6,6,3054,2061),(pella_50)),
'f3_30000.tif':((33,255),(6, 9, 3066, 1980),(pella_50)),
'f3_30000_2.tif':((35,255),(6, 21, 3066, 2016),(pella_50)),
'f3_30000_3.tif':((41,255),(6,9,3057,2067),(pella_50)),
'f4_10000_low.tif':((41,255),(9,9,3051,2058),(pella_50)),
'f4_10000_high.tif':((45,255),(9,9,3051,2058),(pella_50)),
'f4_30000.tif':((46,255),(15, 15, 3057, 2034), (pella_50)),
'f4_30000_2_low.tif':((38,255),(6,6,3057,2061),(pella_50)),
'f4_30000_2_high.tif':((44,255),(6,6,3057,2061),(pella_50))
}
manual_adjustments['jan_28_13'] = {
'f1_30000_low.tif':((62,255),(1323,669,1743,1629),(new_18)), #bad image, huge crop
'f1_30000_high.tif':((76,255),(1323,669,1743,1629),(new_18)),
'f3_50000_low.tif':((98,255),(3,258,3063,1722),(new_18)),#HUGE AGGREGATES
'f3_50000_high.tif':((105,255),(3,258,3063,1722),(new_18)),
'f3_100000_low.tif':((98,255),(3,123,3060,1713),(new_18)),
'f3_100000_high.tif':((117,255),(3,123,3060,1713),(new_18)),
'f4_30000_low.tif':((50,255),(3,3,3063,1992),(new_18)),
'f4_30000_high.tif':((70,255),(3,3,3063,1992),(new_18)),
'f4_49480_low.tif':((73,255),(3,6,3063,1989),(new_18)),
'f4_49480_high.tif':((84,255),(3,6,3063,1989),(new_18))
}
manual_adjustments['jan_29_13'] = {
# Changed the fx_date_mag_low ---> fx_mag_low for ones i will be using
'f1_1_29_10000_low.tif':((81,255),(3,6,3063,984),(new_22)),
'f1_1_29_10000_high.tif':((92,255),(3,6,3063,984),(new_22)),
'f1_30000_low.tif':((77,255),(39,6,3027,2067),(new_22)),
'f1_30000_high.tif':((87,255),(39,6,3027,2067),(new_22)),
'f1_50000_low.tif':((79,255),(9,9,3045,2028),(new_22)),
'f1_50000_high.tif':((84,255),(9,9,3045,2028),(new_22)),
'f3_1_29_10000_low.tif':((78,255),(3,3,3063,2073),(new_22)),
'f3_1_29_10000_high.tif':((82,255),(3,3,3063,2073),(new_22)),
'f3_30000_low.tif':((73,255),(3,3,3063,2046),(new_22)),
'f3_30000_high.tif':((80,255),(3,3,3063,2046),(new_22)),
'f3_100000_low.tif':((86,255),(0,27,3069,1968),(new_22)),
'f3_100000_high.tif':((108,255),(0,27,3069,1968),(new_22)),
'f4_1_29_10000_low.tif':((45,255),(3,3,3063,1989),(new_22)),
'f4_1_29_10000_high.tif':((54,255),(3,3,3063,1989),(new_22)),
'f4_30000_low.tif':((40,255),(9,9,3054,1983),(new_22)),
'f4_30000_high.tif':((45,255),(9,9,3054,1983),(new_22))
}
manual_adjustments['feb_4_13'] = {
'f2_30000.tif':((86,255), (15, 18, 3057, 2019), (new_22)),
'f4_30000.tif':((77,255), (9, 15, 3063, 2016), (new_22))
}
manual_adjustments['feb_2_13'] = {
'f2_30000.tif':((76,255), (18, 21, 3054, 2025), (new_22)),
'f2_40000.tif':((74,255), (12, 30, 3060, 2001), (new_22)),
'f3_30000.tif':((86,255), (15, 9, 3057, 2028), (new_22))
}
manual_adjustments['feb_8_13'] = {
'f1_30000_low.tif':((44,255),(9,609,3057,1689),(new_22)),
'f1_30000_high.tif':((54,255),(9,609,3057,1689),(new_22)),
'f2_30000_low.tif':((49,255),(None),(new_22)), #THIS ONE USES BOTH TYPES AUNPS
'f2_30000_high.tif':((57,255),(None),(new_22)),
'f2_30000_2_low.tif':((59,255),(None),(new_22)), #THIS ONE USES BOTH TYPES ANNPS
'f3_37000_lineint_low.tif':((101,255),(1,213,1021,553),(new_22)),
'f3_37000_lineint_high.tif':((111,255),(1,213,1021,553),(new_22)),
'f4_50000_low.tif':((41,255),(3,120,3063,2178),(new_22)),
'f4_50000_high.tif':((44,255),(3,120,3063,2178),(new_22))
}
manual_adjustments['feb_25_13'] = {
'f3_30000_low.tif':((74,255),(3,3,3063,2004),(new_22)),
'f3_30000_high.tif':((89,255),(3,6,3060,2001),(new_22)),
'f3_30000_2_low.tif':((90,255),(12,39,3054,1968),(new_22)),
'f3_30000_high.tif':((111,255),(12,39,3054,1968),(new_22)),
'f4_30000_2_low.tif':((59,255),(6,6,3063,2001),(new_22)), ##blurry image
'f4_30000_2_high.tif':((73,255),(6,6,3063,2001),(new_22)), ##blurry image
'f4_30000_3_low.tif':((68,255),(3,6,3063,2004),(new_22)),
'f4_30000_3_high.tif':((83,255),(6,6,3063,2004),(new_22)),
'f4_30000_4_low.tif':((67,255),(3,3,3063,2007),(new_22)),
'f4_30000_4_high.tif':((79,255),(3,3,3063,2007),(new_22))
}
manual_adjustments['feb_26_13'] = {
'f1_30000.tif':((104,255),(18,9,2016,1989),(new_22)),
'f1_30000_2_low.tif':((120,255),(3,6,3060,2001),(new_22)),
'f1_30000_2_high.tif':((135,255),(3,6,3060,2001),(new_22)),
'f4_83000.tif':((66,255), (201,57,1713,1485), (new_22)) #THIS ONE has lots of gunk, hopefully crop is good engou to get it working
}
manual_adjustments['march_7_13'] = {
'F1_30000_low.tif':((106,255),(20, 40, 3016, 1920),(new_22)), #With large aggregate
'F1_30000_high.tif':((119,255),(48,44,1996,1856),(new_22)), #Double check
#'F1_30000_low.tif':((),(48,44,1996,1856),(new_22)), #Without large aggregate GOOD EXAMPLE
#'F1_30000_high.tif':((),(48,44,1996,1856),(new_22)), #Without large aggregate GOOD EXAMPLE
'F1_100000_low.tif':((100,255),(36, 44, 2940, 1936),(new_22)),
'F1_100000_high.tif':((110,255),(36, 44, 2940, 1936),(new_22)),
'F2_30000_low.tif':((100,255),(264,56,1432,1848),(new_22)),
'F2_30000_high.tif':((122,255),(264,56,1432,1848),(new_22)),
'F2_30000_2_low.tif':((101,255),(52,52,2176,1904),(new_22)),
'F2_30000_2_high.tif':((125,255),(52,52,2176,1904),(new_22)),
'F2_30000_3_low.tif':((112,255),(32,32,2036,1932),(new_22)),
'F2_30000_3_high.tif':((118,255),(32,32,2036,1932),(new_22)),
'F2_72600_low.tif':((104,255),(48, 60, 3024, 1924),(new_22)), #Doublechek none
'F2_72600_high.tif':((115,255),(48, 60, 3024, 1924),(new_22)),
}
manual_adjustments['apr_29_13'] = {
'f1_30000.tif':((142,255), (21, 18, 3051, 2133), (new_22)),
'f2_30000.tif':((130,255), (3, 9, 3069, 2040), (new_22)),
'f2_100000.tif':((143,255), (2, 4, 1022, 708), (new_22))
}
manual_adjustments['sept_4_13_UV50'] = {
'f1_30k_2_auto.tif':((None), (3, 0, 3069, 1452), (new_22)),
'f1_30k_2.tif':((145,255), (3, 0, 3069, 1452), (new_22)),
'f1_30k_auto.tif':((None), (None), (new_22)),
'f1_30k.tif':((129,255), (None), (new_22))
}
manual_adjustments['sept_5_13_UV50'] = {
'f3_30000.tif':((126,255), (21, 177, 3051, 1767), (new_22))
}
manual_adjustments['sept_11_13_UV50'] = {
'f1_30k_1_auto.tif':((None), (6, 0, 3066, 1989), (new_22)),
'f1_30k_1.tif':((107,255), (6, 0, 3066, 1989), (new_22)),
'f1_30k_2_auto.tif':((None), (0, 3, 3072, 1983), (new_22)),
'f1_30k_2.tif':((115,255), (0, 3, 3072, 1983), (new_22)),
'f1_b2_30000_auto.tif':((None), (0, 6, 3072, 1962), (new_22)),
'f1_b2_30000.tif':((118,255), (0, 6, 3072, 1962), (new_22)),
}
manual_adjustments['sept_17_13_UV50'] = {
'f3_30000_auto.tif':((None), (0, 3, 3072, 1986), (new_22)),
'f3_30000.tif':((80,255), (0, 3, 3072, 1986), (new_22)),
}
manual_adjustments['sept_19_13_UV50'] = {
'f1_30k.tif':((107,255), (3, 3, 3054, 1944), (new_22)),
'f1_30k_auto.tif':((None), (3, 3, 3054, 1944), (new_22)),
'f1_30k_2.tif':((97,255), (0, 0, 3066, 1995), (new_22)),
'f1_30k_2_auto.tif':((None), (0, 0, 3066, 1995), (new_22)),
}
manual_adjustments['sept_26_13'] = {
'f1_30000.tif': ((54,255), (12, 19, 3047, 1929), (new_22)),
'f1_30000_2.tif':((57,255), (12,12,3045,1911), (new_22)),
'f2_30000_2.tif':((64,255),(18,15,3054,1797),(new_22)),
'f2_30000_Cropoutbottom.tif':((67,255),(135,0,2919,900),(new_22)),
'f2_89380.tif':((58,255),(12,7,997,629),(new_22)),
'f3_30000.tif':((39, 255),(15, 18, 3039, 1893),(new_22)),
'f3_30000_2.tif':((46,255),(42,21,2994,1905),(new_22))
}
manual_adjustments['oct_1_13'] = {
'f1_30000.tif': ((83,255), (0, 6, 3072, 1785), (new_22)),
'f1_30000_auto.tif': ((None), (0, 6, 3072, 1785), (new_22)),
'f1_30000_2.tif': ((79,255), (0, 3, 3066, 1968), (new_22)),
'f1_30000_2_auto.tif': ((None), (0, 3, 3066, 1968), (new_22)),
}
manual_adjustments['oct_3_13'] = {
'f1_30000.tif': ((61,255), (3, 3, 3066, 1986), (new_22)),
'f1_30000_auto.tif': ((None), (3, 3, 3066, 1986), (new_22)),
'f1_30000_2.tif': ((66,255), (0, 3, 3063, 2010), (new_22)),
'f1_30000_2_auto.tif': ((None), (0, 3, 3063, 2010), (new_22)),
'f2_30000.tif': ((86,255), (0, 0, 3072, 2010), (new_22)),
'f2_30000_auto.tif': ((None), (0, 0, 3072, 2010), (new_22)),
'f2_30000_2.tif': ((65,255), (3, 0, 3063, 1983), (new_22)),
'f2_30000_2_auto.tif': ((None), (3, 0, 3063, 1983), (new_22)),
}
manual_adjustments['oct_8_13'] = {
'f1_30000.tif': ((63,255), (0, 0, 3072, 2067), (new_22)),
'f1_30000_auto.tif': ((None), (0, 0, 3072, 2067), (new_22)),
'f2_30000.tif': ((83,255), (0, 0, 3069, 1938), (new_22)),
'f2_30000_auto.tif': ((None), (0, 0, 3069, 1938), (new_22)),
'f3_30000.tif': ((93,255), (756, 0, 2316, 2304), (new_22)),
'f3_30000_auto.tif': ((None), (756, 0, 2316, 2304), (new_22)),
}
manual_adjustments['oct_9_13'] = {
#'.tif':(( ,255), (), (new_22)),
#'.tif':(( ,255), (), (new_22)),
#'.tif':(( ,255), (), (new_22)),
#'.tif':((, 255), (), (new_22))
}
manual_adjustments['oct_15_13'] = {
'f1_30000.tif': ((114,255),(0, 6, 3072, 1959),(new_22)),
'f2_30000.tif': ((105,255),(0, 0, 3072, 1989),(new_22))
}
manual_adjustments['oct_16_13'] = {
# Adam, I gave some try on these low coverage ones.
# The brightness has almost normal distribution. So not sure if the thresholding works good or not.
'f1_30000.tif': ((84, 255),(1587, 219, 1485, 2004),(new_22)),
'f2_30000.tif': ((78, 255),(0, 0, 3072, 1986),(new_22))
}
manual_adjustments['oct_17_13'] = {
# f2_3000_artifacts.tif is very shaky due to charging. Hence only can pick a very small slice to do threshold.
# This may lead to inaccurate results. Similar with f3_3000_lessartifacts.tif.
'f1_30000.tif': ((68, 255),(1236, 186, 1836, 1815),(new_22)),
'f2_30000_artifacts.tif': ((76, 255),(6, 264, 3057, 282),(new_22)),
'f2_30000_lessartifacts.tif': ((77,255),(0, 636, 3072, 1170),(new_22))
}
manual_adjustments['oct_19_13_abridged'] = { #There are several other images, but they need cropped
'f1_53700.tif':((179, 255), (19, 29, 3053, 1924), (new_22)),
'f1_30000.tif':((142, 255), (9, 15, 3048, 1587), (new_22)),
'f2_30000_good_finally.tif':((174, 255), (12, 18, 3039, 1950), (new_22)),
'f3_30000_good_finally.tif':((167, 255), (4, 12, 3052, 1960), (new_22))
}
manual_adjustments['oct_22_13'] = {
'f1_80000.tif':((164, 255), (None), (new_22)),
'f3_30000_3.tif':((120,255), (9, 14, 3063, 1570), (new_22)),
'f3_30000_2.tif':((107 ,255), (6, 15, 3066, 1896), (new_22)),
'f3_30000.tif':((121 ,255), (7, 14, 3065, 1898), (new_22)),
'f1_30000.tif':((160, 255), (4, 14, 3068, 768), (new_22)),
'f1_30000_2.tif':((72 ,255), (1100, 24, 1964, 1428), (new_22)),
'f1_30000_3_crop1.tif':((88 ,255), (291, 12, 2772, 519), (new_22)),
'f1_30000_3_crop2.tif':((88 ,255), (1047, 687, 2010, 1602), (new_22))
}
# 20 refers to twenty percent AuNP solution concentration
manual_adjustments['oct_26_13_20'] = {
'f1_30000_1.tif':((51, 255), (0, 0, 1584, 2032), (new_22)),
'f1_30000_2.tif':((66, 255), (144, 304, 1604, 1732), (new_22)),
'f2_30000.tif':((128, 255), (0, 0, 2192, 2020), (new_22)),
'f3_30000_1.tif':((108, 255), (0, 308, 2468, 1724), (new_22)),
'f3_30000_2.tif':((98, 255), (0, 0, 3072, 2016), (new_22)),
}
# 35 refers to twenty percent AuNP solution concentratio
manual_adjustments['oct_26_13_35'] = {
'f1_30000.tif':((107, 255), (930, 0, 2142, 2304), (new_22)),
'f2_30000.tif':((82, 255), (0, 0, 3066, 2019), (new_22)),
'f3_30000_1.tif':((41, 255), (0, 0, 3072, 2028), (new_22)),
'f3_30000_2.tif':((77, 255), (0, 0, 3072, 2028), (new_22)),
}
manual_adjustments['oct_30_13'] = {
# 10% fibers
'f1_30000_10perc.tif':((145 ,255), (699, 3, 2367, 2295), (new_22)),
'f1_30000_LOWRES.tif':((135 ,255), (138, 2, 884, 763), (new_22)),
'f1_30000_10perc_3.tif':((117,255), (39,33,2658,1974), (new_22)),
'f1_30000_10perc_4.tif':((107,255), (18,24,3051,2022), (new_22)),
'f1_30000_10perc_5.tif':((94,255), (12, 15, 3045, 2001), (new_22)),
'f2_30000_10perc.tif':((106 ,255), (435, 6, 2631, 2292), (new_22)),
'f2_30000_10perc_2.tif':((121 ,255), (3, 6, 3063, 1479), (new_22)),
'f2_30000_10perc_3_croptop.tif':((107,255), (12,15,3060,2028), (new_22)),
# 20% fibers
'f3_30000_20perc.tif':((82 ,255), (3, 3, 2421, 1512), (new_22)),
'f3_30000_20perc_lowres.tif':((74 ,255), (1, 1, 1021, 668), (new_22)),
'f3_30000_20perc_lowres_2.tif':((67 ,255), (1, 1, 1021, 514), (new_22)),
'f3_30000_20perc_2.tif':((57,255), (24,21,3048,1284), (new_22)),
'f3_30000_20perc_midres.tif':((52,255), (26,12,1998,1352), (new_22)),
'f3_30000_20perc_midres_2.tif':((48,255), (22,12,2026,1332), (new_22)),
'f4_30000_20perc.tif':((80,255), (369, 27, 2703, 2004), (new_22)),
'f4_30000_20perc_2.tif':((78,255), (9, 9, 3063, 1991), (new_22)),
# 35% fibers
'f5_30000_35perc.tif':((110,255), (4,18,3030,1983), (new_22)),
'f5_30000_35perc_2.tif':((101 ,255), (12, 45, 3048, 1956), (new_22)),
'f5_30000_35perc_3.tif':((95,255), (3, 15, 3069, 1980), (new_22)),
'f6_30000_35perc.tif':((113,255), (12, 12, 3060, 1989), (new_22)),
'f6_30000_35perc_2.tif':((95, 255), (885, 21, 2187, 2283), (new_22))
}
manual_adjustments['nov_1_13'] = {
#Fibers 1/2 PH10
'f1_30000_ph10.tif':((153,255), (9,6,3063,1707), (new_22)),
'f1_30000_2_ph10.tif':((175,255), (4,8,1300,1894), (new_22)),
'f1_30000_3_ph10.tif':((149,255), (16,4,3040,1888), (new_22)),
'f2_30000_1_ph10.tif':((136,255), (6, 6, 3051, 1917), (new_22)),
'f2_30000_2_ph10.tif':((134,255), (6, 6, 3066, 1926), (new_22)),
#Fibers 3/4 PH4
'f3_30000_1_ph4.tif':((119 ,255), (18, 15, 3042, 1917), (new_22)),
'f3_30000_2_ph4.tif':((111, 255), (9, 0, 3063, 1932), (new_22)),
'f3_30000_3_ph4.tif':((115,255), (9, 6, 3063, 1923), (new_22)),
'f3_30000_4_ph4.tif':((128, 255), (6, 6, 3051, 1923), (new_22)),
'f4_30000_1_ph4.tif':((144 ,255), (18, 3, 3054, 1929), (new_22)),
'f4_30000_2_ph4.tif':((133, 255), (24, 3, 3048, 1932), (new_22)),
'f4_30000_3_ph4.tif':((136 ,255), (3, 1, 1018, 641), (new_22)),
'f4_30000_bumpyback_ph4.tif':((133, 255), (9, 9, 3051, 1920), (new_22))
#For 'f4_30000_3_ph4.tif' and 'f4_30000_bumpyback_ph4.tif',
#their background is too bumpy to get good threshold."
}
manual_adjustments['nov_2_13'] = {
#Fibers 1/2/3 PH10
'f1_30000.tif':((130 ,255), (9, 6, 3036, 1944), (new_22)),
'f1_30000_2.tif':((129 ,255), (6, 6, 3066, 1953), (new_22)),
'f2_30000.tif':((147 ,255), (6, 6, 3057, 1950), (new_22)),
'f3_30000.tif':((159 ,255), (6, 6, 3066, 1956), (new_22)),
#Fibers 4/5/6 PH4
'f4_30000.tif':((128 ,255), (6, 6, 3063, 1953), (new_22)),
'f4_30000_2.tif':((125 ,255), (3, 6, 3069, 1953), (new_22)),
'f4_52050_mediumres.tif':((131 ,255), (4, 2, 2044, 1310), (new_22)),
'f5_30000.tif':((136 ,255), (9, 6, 3063, 1956), (new_22)),
'f5_30000_2.tif':((126 ,255), (6, 6, 3066, 1953), (new_22)),
'f6_30000.tif':((146 ,255), (6, 3, 3066, 1956), (new_22)),
'f6_60840_lowres_highqual.tif':((139 ,255), (2, 4, 1022, 652), (new_22)),
}
manual_adjustments['SCIKIT_TEST']={
'WATERSHED_8_b1_f3_100k_high.tif':((141 ,255), (2, 3, 1019, 597),(old_30)),
'WATERSHED_8_b2_f2_100k2_high.tif':((169 ,255), (7, 211, 650, 456),(old_30)),
'WATERSHED_f3_100000_low.tif':((98,255),(3,123,3060,1713),(new_18)),
'WARPED_8_b3_f4_100k3_high.tif':((155 ,255), (2, 11, 1016, 590),(old_30)),
'WARPED_f2_b1_50k21_high.tif': ((121, 255),(6, 9, 1007, 625),(old_30)),
'LOWCONTRAST_f3_30000_2.tif':((35,255),(6, 21, 3066, 2016),(pella_50)),
'LOWCONTRAST_f1_30000_low.tif':((64,255),(12,12,3051,2049),(pella_50)),
'LOWCONTRAST_f4_30000_low.tif':((40,255),(9,9,3054,1983),(new_22)),
'NONCIRC-DARK_f2_30000_low.tif':((67,255),(6,9,2967,2046),(pella_50)),
'NICE_f1_30500.tif':((121,255),(30, 30, 3030, 1872),(old_30)),
'NICE_f2_b1_100k21_high.tif':((145, 255),(5, 18, 1012, 614),(old_30)),
}
manual_adjustments['apr_25_14'] = {
'F1_30000_1.tif':((180 ,255), (12, 9, 3060, 1983), (new_22)),
'F1_30000_2.tif':((184,255), (6, 9, 3066, 1986), (new_22)),
'F2_30000_1.tif':((177,255), (6, 9, 3066, 1995), (new_22)),
'F2_30000_2.tif':((136,255), (6, 9, 3066, 1995), (new_22))
}
manual_adjustments['apr_28_14'] = {
'F1_30000_1.tif':((113,255), (0, 6, 3072, 1998), (new_22)),
'F1_30000_2.tif':((117,255), (0, 6, 3072, 1998), (new_22)),
'F2_30000_1.tif':((148,255), (0, 6, 3072, 1998), (new_22)),
'F2_30000_2.tif':((147,255), (0, 6, 3072, 1998), (new_22)),
'F3_30000_1.tif':((139,255), (0, 6, 3072, 1998), (new_22)),
'F3_30000_2.tif':((145,255), (0, 6, 3072, 1998), (new_22)),
'F4_30000_1.tif':((158,255), (0, 6, 3072, 1998), (new_22)),
'F4_30000_2.tif':((152,255), (0, 6, 3072, 1998), (new_22)),
'F3_50000_1.tif':((139,255), (0, 15, 3072, 1980), (new_22)),
'F3_50000_2.tif':((150,255), (6, 3, 3066, 2004), (new_22)),
}
manual_adjustments['may_6_2014'] = {
'f1_30000_1.tif':((200,255), (0, 6, 3072, 1998), (new_22)),
'f1_30000_2.tif':((199,255), (0, 6, 3072, 1998), (new_22)),
'f2_30000_1.tif':((140,255), (0, 6, 3072, 1998), (new_22)),
'f2_30000_2.tif':((142,255), (0, 6, 3072, 1998), (new_22)),
'f2_30000_3.tif':((138,255), (0, 6, 3072, 1998), (new_22)),
'f2_30000_artifact.tif':((145,255), (0, 6, 3072, 1998), (new_22)),
'f2_30000_mishape.tif':((143,255), (0, 6, 3072, 1998), (new_22)),
'f3_30000_1.tif':((185,255), (0, 6, 3072, 1998), (new_22)),
'f3_30000_2.tif':((151,255), (0, 6, 3072, 1998), (new_22)),
'f3_30000_3.tif':((146,255), (0, 6, 3072, 1998), (new_22)),
'f4_30000_1.tif':((123,255), (0, 6, 3072, 1998), (new_22)),
'f4_30000_2.tif':((133,255), (0, 6, 3072, 1998), (new_22)),
'f4_30000_3.tif':((116,255), (0, 6, 3072, 1998), (new_22)),
'f5_30000_1.tif':((111,255), (360, 57, 1665, 1002), (new_22)),
'f5_30000_2.tif':((128,255), (102, 243, 1227, 1332), (new_22)),
'f5_30000_3.tif':((133,255), (0, 6, 3072, 1998), (new_22)),
'f4_50000.tif':((132,255), (3, 6, 3069, 1971), (new_22)),
'f5_50000.tif':((138,255), (3, 6, 3069, 1971), (new_22))
}
manual_adjustments['may_9_14'] = {
'f1_30000_1.tif':((120,255), (0, 0, 3072, 2004), (new_22)),
'f1_30000_2.tif':((123,255), (0, 0, 3072, 2004), (new_22)),
'f1_30000_3.tif':((123,255), (0, 0, 3072, 2004), (new_22)),
'f2_30000_1.tif':((102,255), (0, 0, 3072, 1996), (new_22)),
'f2_30000_2.tif':((141,255), (0, 0, 3072, 2004), (new_22)),
'f2_30000_artifact.tif':((118,255), (0, 860, 3072, 1140), (new_22)),
'f3_30000_1.tif':((152,255), (0, 0, 3072, 1948), (new_22)),
'f3_30000_2.tif':((153,255), (0, 0, 3072, 1948), (new_22)),
'f4_30000_1.tif':((157,255), (0, 0, 3072, 1948), (new_22)),
'f4_30000_2.tif':((160,255), (0, 0, 3072, 1948), (new_22)),
'f1_50000_1.tif':((122,255), (0, 0, 3072, 2004), (new_22)),
'f1_50000_2.tif':((126,255), (0, 0, 3068, 1552), (new_22)),
'f1_50000_3.tif':((127,255), (0, 0, 3072, 1724), (new_22)),
'f2_50000_1.tif':((148,255), (0, 0, 3072, 2004), (new_22)),
'f2_50000_2.tif':((150,255), (0, 0, 3072, 2004), (new_22)),
'f3_50000_1.tif':((153,255), (0, 0, 3072, 1944), (new_22)),
'f3_50000_artifact.tif':((150,255), (0, 0, 3072, 1520), (new_22))
}
manual_adjustments['july_10_14'] = {
'f1_60000.tif':((165,255), (492, 294, 2580, 1743), (new_22)),
'f1_30000.tif':((151,255), (1080, 247, 1699, 1751), (new_22)),
'f2_30000.tif':((183,255), (0, 0, 3072, 1956), (new_22)),
'f2_30000_2.tif':((176,255), (0, 0, 3072, 1956), (new_22)),
'f3_30000.tif':((190,255), (0, 0, 3072, 1956), (new_22)),
'f3_30000_2.tif':((192,255), (0, 0, 3072, 1956), (new_22)),
'f4_30000.tif':((165,255), (0, 0, 3072, 1956), (new_22)),
'f4_30000_2.tif':((139,255), (0, 0, 3072, 1956), (new_22)),
'f5_30000.tif':((179,255), (0, 0, 3072, 1956), (new_22)),
'f5_30000_2.tif':((176,255), (0, 0, 3072, 1956), (new_22)),
'f6_30000.tif':((160,255), (0, 0, 3072, 1956), (new_22)),
'f6_30000_2.tif':((149,255), (0, 0, 3072, 1956), (new_22)),
}