From 0ce1638218b838b13f5c748c12d25125f4914918 Mon Sep 17 00:00:00 2001 From: Oliver Gurney-Champion Date: Wed, 24 Jul 2024 08:47:26 +0200 Subject: [PATCH 1/6] updated abdominal phantom to include more tissue and be properly oriented --- .gitignore | 4 +++- phantoms/MR_XCAT_qMRI/sim_ivim_sig.py | 18 +++++++++++++++--- utilities/data_simulation/Download_data.py | 2 +- 3 files changed, 19 insertions(+), 5 deletions(-) diff --git a/.gitignore b/.gitignore index 2df670a..0c9170c 100644 --- a/.gitignore +++ b/.gitignore @@ -21,4 +21,6 @@ md5sums.txt .cache nosetests.xml coverage.xml -*.pyc \ No newline at end of file +*.pyc +phantoms/MR_XCAT_qMRI/*.json +phantoms/MR_XCAT_qMRI/*.txt \ No newline at end of file diff --git a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py index e3c5635..53f6656 100644 --- a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py +++ b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py @@ -23,7 +23,7 @@ def phantom(bvalue, noise, TR=3000, TE=40, motion=False, rician=False, interleav # Access the variables in the loaded .mat file XCAT = mat_data['IMG'] - XCAT = XCAT[0:-1:2,0:-1:2,10:160:4] + XCAT = XCAT[-1:0:-2,-1:0:-2,10:160:4] D, f, Ds = contrast_curve_calc() S, Dim, fim, Dpim, legend = XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds) @@ -95,15 +95,19 @@ def contrast_curve_calc(): D[8] = 3e-3 # 8 Blood ra D[10] = 1.37e-3 # 8 Muscle: 10.3389/fresc.2022.910068 D[13] = 1.5e-3 # 13 liver: Delattre et al. doi: 10.1097/RLI.0b013e31826ef901 + D[14] = 3.0e-3 # 13 Galbladder D[17] = 1.67e-3 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421 D[18] = 1.67e-3 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421 D[20] = 1.5e-3 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586 + D[21] = 2.0e-3 # 21 stomach content D[22] = 1.3e-3 # 22 Pancreas (from literature) D[23] = 2.12e-3 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519 D[24] = 2.09e-3 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519 D[25] = 2.12e-3 # 23 left kydney cortex : van Baalen et al. Doi: jmri.25519 D[26] = 2.09e-3 # 23 left kydney medulla : van Baalen et al. Doi: jmri.25519 D[30] = 1.3e-3 # 30 spleen : Taimouri et al. Doi: 10.1118/1.4915495 + D[34] = 4.1e-4 # 34 spinal cord :doi: 10.3389/fonc.2022.961473 + D[35] = 0.43e-3 # 35 Bone marrow : https://pubmed.ncbi.nlm.nih.gov/30194746/ D[36] = 3e-3 # 36 artery D[37] = 3e-3 # 37 vein D[40] = 1.31e-3 # 40 asc lower intestine : Hai-Jing et al. doi: 10.1097/RCT.0000000000000926 @@ -124,15 +128,19 @@ def contrast_curve_calc(): f[8] = 1.00 # 8 Blood ra f[10] = 0.10 # 8 Muscle: 10.3389/fresc.2022.910068 f[13] = 0.11 # 13 liver : Delattre et al. doi: 10.1097/RLI.0b013e31826ef901 + f[14] = 0 # 13 Gal f[17] = 0.32 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421 f[18] = 0.32 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421 f[20] = 0.3 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586 + f[21] = 0.0 # 20 stomach content f[22] = 0.15 # 22 Pancreas (from literature) f[23] = 0.097 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519 f[24] = 0.158 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519 f[25] = 0.097 # 23 left kydney cortex : van Baalen et al. Doi: jmri.25519 f[26] = 0.158 # 23 left kydney medulla : van Baalen et al. Doi: jmri.25519 f[30] = 0.2 # 30 spleen : Taimouri et al. Doi: 10.1118/1.4915495 + f[34] = 0.178 # 34 spinal cord :doi: 10.3389/fonc.2022.961473 + f[35] = 0.145 # 35 Bone marrow : https://pubmed.ncbi.nlm.nih.gov/30194746/ f[36] = 1.0 # 36 artery f[37] = 1.0 # 37 vein f[40] = 0.69 # 40 asc lower intestine : Hai-Jing et al. doi: 10.1097/RCT.0000000000000926 @@ -153,15 +161,19 @@ def contrast_curve_calc(): Ds[8] = 0.1 # 8 Blood ra Ds[10] = 0.0263 # 8 Muscle: 10.3389/fresc.2022.910068 Ds[13] = 0.1 # 13 liver: Delattre et al. doi: 10.1097/RLI.0b013e31826ef901 + Ds[14] = 0.1 # 14 Gal Ds[17] = 0.03 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421 Ds[18] = 0.03 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421 Ds[20] = 0.012 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586 + Ds[21] = 0.1 # 20 stomach content Ds[22] = 0.01 # 22 Pancreas (from literature) Ds[23] = 0.02 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519 Ds[24] = 0.019 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519 Ds[25] = 0.02 # 23 left kydney cortex : van Baalen et al. Doi: jmri.25519 Ds[26] = 0.019 # 23 left kydney medulla : van Baalen et al. Doi: jmri.25519 Ds[30] = 0.03 # 30 spleen : Taimouri et al. Doi: 10.1118/1.4915495 + Ds[34] = 0.0289 # 34 spinal cord :doi: 10.3389/fonc.2022.961473 + Ds[35] = 0.05 # 35 Bone marrow : Ds[36] = 0.1 # 36 artery Ds[37] = 0.1 # 37 vein Ds[40] = 0.029 # 40 asc lower intestine : Hai-Jing et al. doi: 10.1097/RCT.0000000000000926 @@ -261,7 +273,7 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True): 73: 'Pancreas tumor', } ############################################################################### - np.random.seed(42) + np.random.seed(41) Tissue = np.zeros((74, 4)) Tissue[1] = [1030, 40, 1471, 47] Tissue[2] = [1030, 40, 1471, 47] @@ -427,7 +439,7 @@ def parse_bvalues_file(file_path): # sig = np.flip(sig,axis=0) # sig = np.flip(sig,axis=1) res=np.eye(4) - res[2]=2 + res[2,2]=2 voxel_selector_fraction = 0.5 D, f, Ds = contrast_curve_calc() diff --git a/utilities/data_simulation/Download_data.py b/utilities/data_simulation/Download_data.py index d03d8eb..c28886b 100644 --- a/utilities/data_simulation/Download_data.py +++ b/utilities/data_simulation/Download_data.py @@ -2,7 +2,7 @@ import os import subprocess import time - +import zenodo_get def unzip_file(zip_file_path, extracted_folder_path): # Open the zip file From af522292095a4d939ac3f45985eb4e9183d44b0e Mon Sep 17 00:00:00 2001 From: Oliver Gurney-Champion Date: Wed, 7 Aug 2024 17:19:36 +0200 Subject: [PATCH 2/6] Update sim_ivim_sig.py --- phantoms/MR_XCAT_qMRI/sim_ivim_sig.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py index 53f6656..0bfcfe2 100644 --- a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py +++ b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py @@ -273,7 +273,7 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True): 73: 'Pancreas tumor', } ############################################################################### - np.random.seed(41) + np.random.seed(42) Tissue = np.zeros((74, 4)) Tissue[1] = [1030, 40, 1471, 47] Tissue[2] = [1030, 40, 1471, 47] From a5267de2abe7a43fca21651a408c66b82e7328d1 Mon Sep 17 00:00:00 2001 From: Oliver Gurney-Champion Date: Tue, 13 Aug 2024 17:25:07 +0200 Subject: [PATCH 3/6] updated generic.json files in test --- tests/IVIMmodels/unit_tests/generic.json | 972 ++++++++------- tests/IVIMmodels/unit_tests/generic_four.json | 972 ++++++++------- tests/IVIMmodels/unit_tests/generic_one.json | 1070 ++++++++++------- .../IVIMmodels/unit_tests/generic_three.json | 923 ++++++++------ tests/IVIMmodels/unit_tests/generic_two.json | 1070 ++++++++++------- 5 files changed, 2836 insertions(+), 2171 deletions(-) diff --git a/tests/IVIMmodels/unit_tests/generic.json b/tests/IVIMmodels/unit_tests/generic.json index 47fcb3e..cb95c91 100644 --- a/tests/IVIMmodels/unit_tests/generic.json +++ b/tests/IVIMmodels/unit_tests/generic.json @@ -1,28 +1,28 @@ { "Myocardium LV": { "noise": 0.0005, - "D": 0.0024, + "D": 0.0023999999999999994, "f": 0.14999999999999997, "Dp": 0.08, "data": [ - 0.37020853964957995, - 0.36495023994839576, - 0.36040161395777776, - 0.3482649413062642, - 0.3311252519245551, - 0.31128471484956144, - 0.29753771205592827, - 0.27895404495875237, - 0.2627838930390298, - 0.24600672258762385, - 0.21960592872343127, - 0.17325350570406992, - 0.13578433027277387, - 0.12026630133722724, - 0.08269998770527108, - 0.0583466003590057, - 0.04025758982493964, - 0.028838742483508213 + 0.370013999641509, + 0.36482466842951006, + 0.36010988409575734, + 0.34740847446945766, + 0.33136451957650964, + 0.31089405369851425, + 0.29804908750859893, + 0.27995600724709835, + 0.26252143771186937, + 0.24666592033309503, + 0.21917332306214563, + 0.1724110429210971, + 0.1358492660318187, + 0.1204254159400839, + 0.08379632153652919, + 0.05929197197551733, + 0.041777243745743924, + 0.027800733137212853 ] }, "myocardium RV": { @@ -31,50 +31,50 @@ "f": 0.14999999999999997, "Dp": 0.07999999999999999, "data": [ - 0.36977273246921033, - 0.36537365912605413, - 0.3595159042305869, - 0.34752698949768374, - 0.33173079647378234, - 0.3110608405629893, - 0.29805095418985367, - 0.27952927870925937, - 0.2623759963395676, - 0.2465802608039568, - 0.2205672287951045, - 0.17374944003807846, - 0.13502827555889882, - 0.12066297243669499, - 0.0836121527856757, - 0.05884198664879518, - 0.041489689098644505, - 0.028319859045401394 + 0.37007090353430494, + 0.3654318511653469, + 0.3593311321034827, + 0.3471760704289119, + 0.331800048955708, + 0.31038967888239116, + 0.2975284138894737, + 0.28029678624968507, + 0.2629787017944134, + 0.2477074293476535, + 0.21918030069371341, + 0.17240151355569833, + 0.13481157088486148, + 0.12101386651518903, + 0.08461414420632037, + 0.057637223546638534, + 0.040948204801287136, + 0.027866188408133565 ] }, "myocardium ra": { "noise": 0.0005, - "D": 0.0015, - "f": 0.07000000000000002, - "Dp": 0.07000000000000002, + "D": 0.0014999999999999998, + "f": 0.07, + "Dp": 0.07, "data": [ - 0.3702523127001939, - 0.36755530947936665, - 0.3655092171111401, - 0.3587682397967246, - 0.35132224032603726, - 0.34087328451399485, - 0.3322050929514831, - 0.31948125995637927, - 0.30728799801895257, - 0.29586365531065567, - 0.2747381860006265, - 0.23736891610574076, - 0.20330679507798272, - 0.18899390991911522, - 0.15183897083022813, - 0.11947654863593715, - 0.0961082153184848, - 0.07618502040438892 + 0.37039922196129116, + 0.36707876023464464, + 0.36630023989666943, + 0.35961941284233506, + 0.3524153633271752, + 0.3397650081696079, + 0.3323498616689556, + 0.3200692875550778, + 0.30722032390589876, + 0.2957698898057959, + 0.2739769628099305, + 0.23730139210569473, + 0.20204592072328714, + 0.1884563649032578, + 0.15129668729942214, + 0.11920401005177417, + 0.09617711548717917, + 0.07609492071178242 ] }, "Blood RV": { @@ -83,24 +83,24 @@ "f": 1.0, "Dp": 0.1, "data": [ - 0.677301342624779, - 0.6130133898159349, - 0.5549567775209086, - 0.41065608429951045, - 0.2485679217237561, - 0.09152471508006849, - 0.03422606076706993, - 0.004391344655692806, - -0.0004185323666306052, - 0.00020745211260014227, - 9.950041472725093e-05, - 0.00033731346702161615, - -0.0004581887966317206, - 3.932025610280517e-05, - 0.0007977517497581966, - -9.674856879304352e-05, - -0.0007204219029777662, - -0.00010866334273215243 + 0.678420732918084, + 0.6130837366851998, + 0.5542825525935415, + 0.4107212329572848, + 0.24966661298560333, + 0.09195259289167305, + 0.03406454697199036, + 0.0050754772261917165, + 8.812813203215076e-06, + -0.0003860541858529662, + 0.0005723360062785865, + 0.0002750142626897616, + 6.602092450189775e-05, + 0.0005070911042906469, + -0.0010201585810508762, + -0.00033545531560461706, + -4.138621780211343e-05, + -3.057038566732644e-05 ] }, "Blood RA": { @@ -109,24 +109,50 @@ "f": 1.0, "Dp": 0.09999999999999998, "data": [ - 0.6784642687872807, - 0.6135371749705592, - 0.5551735492299803, - 0.41181139461379773, - 0.24923005810598367, - 0.0905737104418847, - 0.03324974683655229, - 0.005422829610804135, - 0.0013661550851885077, - -0.00010124567605655351, - -0.0006196825747740377, - -0.000911449851230475, - 4.552359004633976e-06, - 0.00045058131568997706, - -0.0004429879455544712, - 0.00023402108507587148, - 0.0008873455071852579, - -0.0003493718684806242 + 0.6774582990343977, + 0.6129818136077116, + 0.5555044828147361, + 0.41075202308488945, + 0.24975540048325642, + 0.09151771386646716, + 0.0332923686312419, + 0.005021977894440545, + 0.00011382910766974185, + -0.0005345953673385111, + 0.00016057202962279233, + -0.00035291450556717007, + 0.0008226789593080546, + -0.00043362989747228295, + -0.000362292924476757, + -0.0005147600841361719, + 0.00019344887052810314, + 5.962153441482305e-05 + ] + }, + "muscle": { + "noise": 0.0005, + "D": 0.00137, + "f": 0.10000000000000002, + "Dp": 0.026299999999999994, + "data": [ + 0.31031915425567325, + 0.3087684277399869, + 0.30777120453726564, + 0.3037177380906508, + 0.2998977814751397, + 0.2902931644882698, + 0.2822227831923153, + 0.26841834993210845, + 0.2569048391520693, + 0.2464254586264409, + 0.2277657895061223, + 0.19805719023861518, + 0.17229443079859247, + 0.16101991878629085, + 0.1324740607211804, + 0.10651323509008759, + 0.08692551467988802, + 0.07044946804598456 ] }, "Liver": { @@ -135,206 +161,258 @@ "f": 0.11000000000000007, "Dp": 0.1, "data": [ - 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"Dp": 0.009999999999999998, + "Dp": 0.01, "data": [ - 0.3103093353499032, - 0.3086555979462937, - 0.30868551309587694, - 0.3054401417241601, - 0.3000029954428556, - 0.28945134888384705, - 0.2802004082880951, - 0.26178803339645007, - 0.2407823261780593, - 0.2215963893368975, - 0.1882027440790469, - 0.1374763807694227, - 0.10141005432707072, - 0.08739455730843261, - 0.06381550663211193, - 0.035407574842628166, - 0.026744554367110734, - 0.014898384338215711, - 0.010535994594789228, - 0.008640506769047538 + 0.31060435329540415, + 0.3094584757965792, + 0.30832474100445584, + 0.3042959936223251, + 0.29978130740682085, + 0.2892722852052438, + 0.2797646588880654, + 0.26127352462035236, + 0.2402280008257731, + 0.2219366326514906, + 0.18898703828107716, + 0.13854673253820252, + 0.10139613014306591, + 0.08729497024980334, + 0.06511483822308424, + 0.035801090513003356, + 0.025829482019818748, + 0.013678551273955484, + 0.011151583862705075, + 0.00808375532900015 ] }, "config": { From d76735f4a675dbe9e08c9fd654903f5ed507d2f3 Mon Sep 17 00:00:00 2001 From: Oliver Gurney-Champion Date: Wed, 14 Aug 2024 10:38:02 +0200 Subject: [PATCH 4/6] adjusted some of the values for tissue with no signal --- phantoms/MR_XCAT_qMRI/sim_ivim_sig.py | 6 +-- tests/IVIMmodels/unit_tests/generic.json | 40 ++++++++--------- tests/IVIMmodels/unit_tests/generic_four.json | 40 ++++++++--------- tests/IVIMmodels/unit_tests/generic_one.json | 44 +++++++++---------- .../IVIMmodels/unit_tests/generic_three.json | 38 ++++++++-------- tests/IVIMmodels/unit_tests/generic_two.json | 44 +++++++++---------- tests/IVIMmodels/unit_tests/test_ivim_fit.py | 6 ++- 7 files changed, 110 insertions(+), 108 deletions(-) diff --git a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py index 0bfcfe2..e18a932 100644 --- a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py +++ b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py @@ -99,7 +99,7 @@ def contrast_curve_calc(): D[17] = 1.67e-3 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421 D[18] = 1.67e-3 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421 D[20] = 1.5e-3 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586 - D[21] = 2.0e-3 # 21 stomach content + D[21] = 3.0e-3 # 21 stomach content D[22] = 1.3e-3 # 22 Pancreas (from literature) D[23] = 2.12e-3 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519 D[24] = 2.09e-3 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519 @@ -165,7 +165,7 @@ def contrast_curve_calc(): Ds[17] = 0.03 # 17 esophagus : Huang et al. doi: 10.1259/bjr.20170421 Ds[18] = 0.03 # 18 esophagus cont : Huang et al. doi: 10.1259/bjr.20170421 Ds[20] = 0.012 # 20 stomach wall: Li et al. doi: 10.3389/fonc.2022.821586 - Ds[21] = 0.1 # 20 stomach content + Ds[21] = 0.0 # 20 stomach content Ds[22] = 0.01 # 22 Pancreas (from literature) Ds[23] = 0.02 # 23 right kydney cortex : van Baalen et al. Doi: jmri.25519 Ds[24] = 0.019 # 23 right kydney medulla : van Baalen et al. Doi: jmri.25519 @@ -297,7 +297,7 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True): Tissue[19] = [1045.5, 37.3, 1201, 44] Tissue[20] = [981.5, 36, 1232.9, 37.20] #Tissue[20] = [981.5, 36, 1232.9, 37.20] - Tissue[21] = [0, 0, 0, 0] + Tissue[21] = [2500, 1250, 4000, 2000] Tissue[22] = [584, 46, 725, 43] Tissue[23] = [828, 71, 1168, 66] Tissue[24] = [1412, 85, 1545, 81] diff --git a/tests/IVIMmodels/unit_tests/generic.json b/tests/IVIMmodels/unit_tests/generic.json index cb95c91..b6b2f5f 100644 --- a/tests/IVIMmodels/unit_tests/generic.json +++ b/tests/IVIMmodels/unit_tests/generic.json @@ -287,28 +287,28 @@ }, "Stomach Contents": { "noise": 0.0005, - "D": 0.002000000000000001, + "D": 0.0030000000000000005, "f": 0.0, - "Dp": 0.10000000000000002, + "Dp": 0.0, "data": [ - 5.80074394810416e-05, - 5.107581409413805e-05, - -0.00012425433616179758, - -0.0003012924365816795, - 0.00012758643047470927, - 0.0004170165250105098, - 8.461158236131148e-05, - -0.00016202394652097316, - -0.000958161107821496, - 0.000452036540223895, - -0.0006338373896442981, - -6.407697371328715e-05, - 6.664092464539553e-05, - 0.0005538785306771071, - -1.2423671933829899e-05, - 0.0004053531904869084, - 7.083433682752305e-05, - 0.0008320566959464623 + 0.5126018871088376, + 0.5110596279871825, + 0.5093535694210771, + 0.5046118029961769, + 0.4975235052032258, + 0.4831126643032834, + 0.4685144470320901, + 0.44098858155273923, + 0.4083164396340143, + 0.3801538814981812, + 0.32617856922898014, + 0.24204450859420612, + 0.17942509249683888, + 0.15492912843811152, + 0.09842158158269289, + 0.06316964601772247, + 0.04009111436010544, + 0.02635011387457495 ] }, "pancreas": { diff --git a/tests/IVIMmodels/unit_tests/generic_four.json b/tests/IVIMmodels/unit_tests/generic_four.json index adbf8b7..f450eeb 100644 --- a/tests/IVIMmodels/unit_tests/generic_four.json +++ b/tests/IVIMmodels/unit_tests/generic_four.json @@ -287,28 +287,28 @@ }, "Stomach Contents": { "noise": 0.0005, - "D": 0.002000000000000001, + "D": 0.0030000000000000005, "f": 0.0, - "Dp": 0.10000000000000002, + "Dp": 0.0, "data": [ - 5.80074394810416e-05, - 5.107581409413805e-05, - -0.00012425433616179758, - -0.0003012924365816795, - 0.00012758643047470927, - 0.0004170165250105098, - 8.461158236131148e-05, - -0.00016202394652097316, - -0.000958161107821496, - 0.000452036540223895, - -0.0006338373896442981, - -6.407697371328715e-05, - 6.664092464539553e-05, - 0.0005538785306771071, - -1.2423671933829899e-05, - 0.0004053531904869084, - 7.083433682752305e-05, - 0.0008320566959464623 + 0.5126018871088376, + 0.5110596279871825, + 0.5093535694210771, + 0.5046118029961769, + 0.4975235052032258, + 0.4831126643032834, + 0.4685144470320901, + 0.44098858155273923, + 0.4083164396340143, + 0.3801538814981812, + 0.32617856922898014, + 0.24204450859420612, + 0.20845143168394226, + 0.15492912843811152, + 0.11435157428178726, + 0.0851282866646102, + 0.06283512716406309, + 0.047328988430565426 ] }, "pancreas": { diff --git a/tests/IVIMmodels/unit_tests/generic_one.json b/tests/IVIMmodels/unit_tests/generic_one.json index 8119de3..e08194e 100644 --- a/tests/IVIMmodels/unit_tests/generic_one.json +++ b/tests/IVIMmodels/unit_tests/generic_one.json @@ -309,30 +309,30 @@ }, "Stomach Contents": { "noise": 0.0005, - "D": 0.002000000000000001, + "D": 0.0030000000000000005, "f": 0.0, - "Dp": 0.10000000000000002, + "Dp": 0.0, "data": [ - -0.0006891569843084475, - -0.000350349205760221, - -0.000917113669609909, - 4.602241579321293e-08, - -0.00018302139591143602, - 0.00018186374664528606, - -0.0004530159152872634, - 2.8535519125183674e-05, - -0.00045237992205407436, - 0.0001590664107331867, - -0.0002977007140224263, - 0.0001680245153855177, - -0.00021378084344275637, - -2.973881510708059e-05, - -0.0005213401147112412, - -0.00018130926334482638, - -0.00029702560689974104, - 0.0001829254096871082, - -6.193284334855272e-05, - 4.118162939074253e-05 + 0.5118547226850481, + 0.5106582029673281, + 0.508560710087629, + 0.5049131414551744, + 0.49721289737683966, + 0.4828775115249182, + 0.46797681953444153, + 0.4411791410183854, + 0.40882222081978176, + 0.3798609113686905, + 0.326514705904602, + 0.24227661008330495, + 0.17914467072875073, + 0.1543455110923273, + 0.09791266513991548, + 0.06258298356389073, + 0.03972325441637818, + 0.025700982588315595, + 0.018842308870977337, + 0.014045788339534756 ] }, "pancreas": { diff --git a/tests/IVIMmodels/unit_tests/generic_three.json b/tests/IVIMmodels/unit_tests/generic_three.json index 61df818..0284f96 100644 --- a/tests/IVIMmodels/unit_tests/generic_three.json +++ b/tests/IVIMmodels/unit_tests/generic_three.json @@ -276,27 +276,27 @@ }, "Stomach Contents": { "noise": 0.0005, - "D": 0.002000000000000001, + "D": 0.0030000000000000005, "f": 0.0, - "Dp": 0.10000000000000002, + "Dp": 0.0, "data": [ - -0.00015283463313758177, - 0.0001016610871739754, - 0.0007074038187109081, - 0.00036841293881897637, - 0.00021476864205758202, - 0.0003864380804761366, - -0.0009806012679601853, - 0.0007615651897909676, - 7.007298111510775e-05, - -0.0007165444873753203, - 0.0004936886427893894, - 0.0018016206647201063, - -0.0004921881101895262, - 0.00032495269107461994, - 0.00036673577745912576, - 7.404966351412328e-05, - 6.03246126200487e-05 + 0.512391045036219, + 0.5111102132602624, + 0.5101852275759499, + 0.5052815083715776, + 0.4976106874148087, + 0.483082085858749, + 0.4674492341817686, + 0.4419121706890512, + 0.4093446737229509, + 0.37898530047058193, + 0.3273060952614138, + 0.24391020623263954, + 0.17886626346200396, + 0.13319696164901507, + 0.09880074103208585, + 0.0677266861434733, + 0.04655725634723901 ] }, "pancreas": { diff --git a/tests/IVIMmodels/unit_tests/generic_two.json b/tests/IVIMmodels/unit_tests/generic_two.json index 795c603..625b082 100644 --- a/tests/IVIMmodels/unit_tests/generic_two.json +++ b/tests/IVIMmodels/unit_tests/generic_two.json @@ -309,30 +309,30 @@ }, "Stomach Contents": { "noise": 0.0005, - "D": 0.002000000000000001, + "D": 0.0030000000000000005, "f": 0.0, - "Dp": 0.10000000000000002, + "Dp": 0.0, "data": [ - -0.0006891569843084475, - -0.000350349205760221, - -0.000917113669609909, - 4.602241579321293e-08, - -0.00018302139591143602, - 0.00018186374664528606, - -0.0004530159152872634, - 2.8535519125183674e-05, - -0.00045237992205407436, - 0.0001590664107331867, - -0.0002977007140224263, - 0.0001680245153855177, - -0.00021378084344275637, - -2.973881510708059e-05, - -0.0005213401147112412, - -0.00018130926334482638, - -0.00029702560689974104, - 0.0001829254096871082, - -6.193284334855272e-05, - 4.118162939074253e-05 + 0.5118547226850481, + 0.5106582029673281, + 0.508560710087629, + 0.5049131414551744, + 0.49721289737683966, + 0.4828775115249182, + 0.46797681953444153, + 0.4411791410183854, + 0.40882222081978176, + 0.3798609113686905, + 0.326514705904602, + 0.24227661008330495, + 0.17914467072875073, + 0.1543455110923273, + 0.11384265783900985, + 0.06258298356389073, + 0.04619990612771922, + 0.025700982588315595, + 0.018842308870977337, + 0.014045788339534756 ] }, "pancreas": { diff --git a/tests/IVIMmodels/unit_tests/test_ivim_fit.py b/tests/IVIMmodels/unit_tests/test_ivim_fit.py index 41a08af..f4ecc2b 100644 --- a/tests/IVIMmodels/unit_tests/test_ivim_fit.py +++ b/tests/IVIMmodels/unit_tests/test_ivim_fit.py @@ -169,6 +169,8 @@ def test_ivim_fit_saved(name, bvals, data, algorithm, xfail, kwargs, tolerances, tolerances = tolerances_helper(tolerances, ratio, data["noise"]) [f_fit, Dp_fit, D_fit] = fit.osipi_fit(signal, bvals) npt.assert_allclose(data['f'], f_fit, rtol=tolerances["rtol"]["f"], atol=tolerances["atol"]["f"]) - npt.assert_allclose(data['D'], D_fit, rtol=tolerances["rtol"]["D"], atol=tolerances["atol"]["D"]) - npt.assert_allclose(data['Dp'], Dp_fit, rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"]) + if data['f']<0.80: # we need some signal for D to be detected + npt.assert_allclose(data['D'], D_fit, rtol=tolerances["rtol"]["D"], atol=tolerances["atol"]["D"]) + if data['f']>0.03: #we need some f for D* to be interpretable + npt.assert_allclose(data['Dp'], Dp_fit, rtol=tolerances["rtol"]["Dp"], atol=tolerances["atol"]["Dp"]) From c45231d244bb41e12c28d85b7274e1ca7b6fccde Mon Sep 17 00:00:00 2001 From: Oliver Gurney-Champion Date: Wed, 14 Aug 2024 13:24:22 +0200 Subject: [PATCH 5/6] updated unit test files to be normalized SNR-wise --- phantoms/MR_XCAT_qMRI/sim_ivim_sig.py | 18 +- tests/IVIMmodels/unit_tests/generic.json | 940 +++++++-------- tests/IVIMmodels/unit_tests/generic_four.json | 940 +++++++-------- tests/IVIMmodels/unit_tests/generic_one.json | 1032 ++++++++--------- .../IVIMmodels/unit_tests/generic_three.json | 894 +++++++------- tests/IVIMmodels/unit_tests/generic_two.json | 1032 ++++++++--------- 6 files changed, 2430 insertions(+), 2426 deletions(-) diff --git a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py index e18a932..df334c3 100644 --- a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py +++ b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py @@ -11,7 +11,7 @@ # code adapted from MAtlab code by Eric Schrauben: https://github.com/schrau24/XCAT-ERIC # This code generates a 4D IVIM phantom as nifti file -def phantom(bvalue, noise, TR=3000, TE=40, motion=False, rician=False, interleaved=False): +def phantom(bvalue, noise, TR=3000, TE=40, motion=False, rician=False, interleaved=False,T1T2=True): np.random.seed(42) if motion: states = range(1,21) @@ -26,7 +26,7 @@ def phantom(bvalue, noise, TR=3000, TE=40, motion=False, rician=False, interleav XCAT = XCAT[-1:0:-2,-1:0:-2,10:160:4] D, f, Ds = contrast_curve_calc() - S, Dim, fim, Dpim, legend = XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds) + S, Dim, fim, Dpim, legend = XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds,T1T2=T1T2) if state == 1: Dim_out = Dim fim_out = fim @@ -187,7 +187,7 @@ def contrast_curve_calc(): return D, f, Ds -def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True): +def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True, T1T2=True): ########################################################################################### # This script converts XCAT tissue values to MR contrast based on the SSFP signal equation. # Christopher W. Roy 2018-12-04 # fetal.xcmr@gmail.com @@ -363,7 +363,6 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True): else: T1 = Tissue[iTissue, 2] T2 = Tissue[iTissue, 3] - if ivim_cont and not np.isnan([D[iTissue], f[iTissue], Ds[iTissue]]).any(): # note we are assuming blood fraction has the same T1 as tissue fraction here for simplicity. Can be changed in future. Dtemp=D[iTissue] @@ -374,8 +373,11 @@ def XCAT_to_MR_DCE(XCAT, TR, TE, bvalue, D, f, Ds, b0=3, ivim_cont = True): ftemp=np.random.rand(1)*0.5 Dstemp=5e-3+np.random.rand(1)*1e-1 S0 = ivim(bvalue,Dtemp,ftemp,Dstemp) - if T1 > 0 or T2 > 0: - MR = MR + np.tile(np.expand_dims(XCAT == iTissue,3),len(S0)) * S0 * (1 - 2 * np.exp(-(TR - TE / 2) / T1) + np.exp(-TR / T1)) * np.exp(-TE / T2) + if T1T2: + if T1 > 0 or T2 > 0: + MR = MR + np.tile(np.expand_dims(XCAT == iTissue,3),len(S0)) * S0 * (1 - 2 * np.exp(-(TR - TE / 2) / T1) + np.exp(-TR / T1)) * np.exp(-TE / T2) + else: + MR = MR + np.tile(np.expand_dims(XCAT == iTissue,3),len(S0)) * S0 Dim = Dim + (XCAT == iTissue) * Dtemp fim = fim + (XCAT == iTissue) * ftemp Dpim = Dpim + (XCAT == iTissue) * Dstemp @@ -415,6 +417,7 @@ def parse_bvalues_file(file_path): parser.add_argument("-n", "--noise", type=float, default=0.0005, help="Noise") parser.add_argument("-m", "--motion", action="store_true", help="Motion flag") parser.add_argument("-i", "--interleaved", action="store_true", help="Interleaved flag") + parser.add_argument("-u", "--T1T2", action="store_true", help="weight signal with T1T2") # note, set this to zero when generating test data for unit testing! args = parser.parse_args() if args.bvalues_file and args.bvalue: @@ -432,10 +435,11 @@ def parse_bvalues_file(file_path): noise = args.noise motion = args.motion interleaved = args.interleaved + T1T2 = args.T1T2 download_data() for key, bvalue in bvalues.items(): bvalue = np.array(bvalue) - sig, XCAT, Dim, fim, Dpim, legend = phantom(bvalue, noise, motion=motion, interleaved=interleaved) + sig, XCAT, Dim, fim, Dpim, legend = phantom(bvalue, noise, motion=motion, interleaved=interleaved,T1T2=T1T2) # sig = np.flip(sig,axis=0) # sig = np.flip(sig,axis=1) res=np.eye(4) diff --git a/tests/IVIMmodels/unit_tests/generic.json b/tests/IVIMmodels/unit_tests/generic.json index b6b2f5f..223c417 100644 --- a/tests/IVIMmodels/unit_tests/generic.json +++ b/tests/IVIMmodels/unit_tests/generic.json @@ -5,24 +5,24 @@ "f": 0.14999999999999997, "Dp": 0.08, "data": [ - 0.370013999641509, - 0.36482466842951006, - 0.36010988409575734, - 0.34740847446945766, - 0.33136451957650964, - 0.31089405369851425, - 0.29804908750859893, - 0.27995600724709835, - 0.26252143771186937, - 0.24666592033309503, - 0.21917332306214563, - 0.1724110429210971, - 0.1358492660318187, - 0.1204254159400839, - 0.08379632153652919, - 0.05929197197551733, - 0.041777243745743924, - 0.027800733137212853 + 1.0001231751746, + 0.9863831981799663, + 0.9736795410767166, + 0.9399687907072308, + 0.8967250611562163, + 0.8404681740089247, + 0.8050090669541026, + 0.7567153344368321, + 0.710120431006179, + 0.6680098450848827, + 0.5928443202089699, + 0.46635060352675767, + 0.3670703137207122, + 0.3255000885344592, + 0.2268720656823917, + 0.1591125315010815, + 0.1114196849818942, + 0.07638861567746785 ] }, "myocardium RV": { @@ -31,24 +31,24 @@ "f": 0.14999999999999997, "Dp": 0.07999999999999999, "data": [ - 0.37007090353430494, - 0.3654318511653469, - 0.3593311321034827, - 0.3471760704289119, - 0.331800048955708, - 0.31038967888239116, - 0.2975284138894737, - 0.28029678624968507, - 0.2629787017944134, - 0.2477074293476535, - 0.21918030069371341, - 0.17240151355569833, - 0.13481157088486148, - 0.12101386651518903, - 0.08461414420632037, - 0.057637223546638534, - 0.040948204801287136, - 0.027866188408133565 + 1.000180079067396, + 0.986990380915803, + 0.972900789084442, + 0.939736386666685, + 0.8971605905354147, + 0.8399637991928016, + 0.8044883933349772, + 0.7570561134394189, + 0.7105776950887231, + 0.6690513540994412, + 0.5928512978405378, + 0.46634107416135884, + 0.36603261857375496, + 0.32608853910956437, + 0.22768988835218287, + 0.1574577830722027, + 0.1105906460374374, + 0.07645407094838856 ] }, "myocardium ra": { @@ -57,24 +57,24 @@ "f": 0.07, "Dp": 0.07, "data": [ - 0.37039922196129116, - 0.36707876023464464, - 0.36630023989666943, - 0.35961941284233506, - 0.3524153633271752, - 0.3397650081696079, - 0.3323498616689556, - 0.3200692875550778, - 0.30722032390589876, - 0.2957698898057959, - 0.2739769628099305, - 0.23730139210569473, - 0.20204592072328714, - 0.1884563649032578, - 0.15129668729942214, - 0.11920401005177417, - 0.09617711548717917, - 0.07609492071178242 + 1.0005083974943823, + 0.9933276431820893, + 0.9888917449810792, + 0.9723245049412418, + 0.9515956772980587, + 0.9193243894352221, + 0.8979671161354167, + 0.8650603283883946, + 0.8311011950802928, + 0.8001863046312927, + 0.7419099058924017, + 0.6400539643681297, + 0.5486982712430136, + 0.5100608251175099, + 0.4081030648058328, + 0.3242680675714864, + 0.25992409130127514, + 0.2068495366721375 ] }, "Blood RV": { @@ -83,20 +83,20 @@ "f": 1.0, "Dp": 0.1, "data": [ - 0.678420732918084, - 0.6130837366851998, - 0.5542825525935415, - 0.4107212329572848, - 0.24966661298560333, - 0.09195259289167305, - 0.03406454697199036, - 0.0050754772261917165, - 8.812813203215076e-06, - -0.0003860541858529662, - 0.0005723360062785865, - 0.0002750142626897616, - 6.602092450189775e-05, - 0.0005070911042906469, + 1.000603693073812, + 0.904606934487691, + 0.818063650190734, + 0.6061350763287074, + 0.36819110032265356, + 0.1355553150583588, + 0.05010509203622437, + 0.0072463289357294755, + 0.00018700717279331042, + -0.0003714271020912267, + 0.0005724345627937243, + 0.00027501426716422045, + 6.60209245021009e-05, + 0.0005070911042906482, -0.0010201585810508762, -0.00033545531560461706, -4.138621780211343e-05, @@ -109,20 +109,20 @@ "f": 1.0, "Dp": 0.09999999999999998, "data": [ - 0.6774582990343977, - 0.6129818136077116, - 0.5555044828147361, - 0.41075202308488945, - 0.24975540048325642, - 0.09151771386646716, - 0.0332923686312419, - 0.005021977894440545, - 0.00011382910766974185, - -0.0005345953673385111, - 0.00016057202962279233, - -0.00035291450556717007, - 0.0008226789593080546, - -0.00043362989747228295, + 0.9996412591901256, + 0.9045050114102029, + 0.8192855804119286, + 0.6061658664563122, + 0.36827988782030663, + 0.1351204360331529, + 0.04933291369547591, + 0.0071928296039783035, + 0.0002920234672598372, + -0.0005199682835767715, + 0.00016067058613793012, + -0.00035291450109271123, + 0.0008226789593082577, + -0.0004336298974722816, -0.000362292924476757, -0.0005147600841361719, 0.00019344887052810314, @@ -135,24 +135,24 @@ "f": 0.10000000000000002, "Dp": 0.026299999999999994, "data": [ - 0.31031915425567325, - 0.3087684277399869, - 0.30777120453726564, - 0.3037177380906508, - 0.2998977814751397, - 0.2902931644882698, - 0.2822227831923153, - 0.26841834993210845, - 0.2569048391520693, - 0.2464254586264409, - 0.2277657895061223, - 0.19805719023861518, - 0.17229443079859247, - 0.16101991878629085, - 0.1324740607211804, - 0.10651323509008759, - 0.08692551467988802, - 0.07044946804598456 + 1.0000325379134485, + 0.9958416765116361, + 0.992251953029248, + 0.9806948706181458, + 0.9652148066834317, + 0.9350173634169726, + 0.9093031036764246, + 0.8665802456277173, + 0.826627506056065, + 0.7926653882373672, + 0.7345335304585094, + 0.6388759729401986, + 0.5565983335419028, + 0.5198757764936984, + 0.4246674084569358, + 0.34442874554680125, + 0.2806458618590227, + 0.22818434184198186 ] }, "Liver": { @@ -161,24 +161,24 @@ "f": 0.11000000000000007, "Dp": 0.1, "data": [ - 0.3756078377852874, - 0.37067125652181937, - 0.3677654958243924, - 0.35700243940277554, - 0.34500415957887226, - 0.3302515861663284, - 0.32172464575305854, - 0.31058135002028275, - 0.29858568623251697, - 0.28865302997932274, - 0.26702170346172016, - 0.23003198509271466, - 0.19803429210290902, - 0.1833033572856394, - 0.14627702927191258, - 0.11790545040742255, - 0.09303820477744078, - 0.07485927220725773 + 0.9998555372369898, + 0.9875516574952231, + 0.9779016913913917, + 0.9500804158170415, + 0.9175743651894844, + 0.8787052561471337, + 0.8562769002282585, + 0.8264801722402275, + 0.7950888834836258, + 0.7668486744904452, + 0.7106617266237084, + 0.6118764736110133, + 0.5266908891237343, + 0.4882123744106181, + 0.3897518246921886, + 0.3123240234096343, + 0.24828458854776078, + 0.19882602755160078 ] }, "gall bladder": { @@ -187,24 +187,24 @@ "f": 0.0, "Dp": 0.09999999999999998, "data": [ - 0.37465833628260115, - 0.37470985800060236, - 0.3741276673659969, - 0.3706235527435471, - 0.3641901011486475, - 0.3535252238103023, - 0.34379226538726515, - 0.3226354918254557, - 0.30003342807804273, - 0.2789249356925978, - 0.24094061267045497, - 0.17738197383031035, - 0.13097498501098148, - 0.11244326334679397, - 0.07311672522753512, - 0.04666453048545899, - 0.028978174203919852, - 0.018615756299741913 + 0.9989060357343036, + 0.9970876206615882, + 0.9946410946403311, + 0.9855774147431635, + 0.9699884929094837, + 0.9414195673254752, + 0.914311705249997, + 0.8599304660085283, + 0.7985053406134563, + 0.7413790056650638, + 0.6389785194259883, + 0.47225570767682007, + 0.34942281984492723, + 0.30046305722115474, + 0.19300343886395055, + 0.12310767410545541, + 0.0777204745744959, + 0.049695219190825604 ] }, "esophagus": { @@ -213,24 +213,24 @@ "f": 0.31999999999999995, "Dp": 0.030000000000000002, "data": [ - 0.37506947489851317, - 0.3714777435366534, - 0.36827829779608984, - 0.3573109714764005, - 0.34059048667914094, - 0.31325028053790294, - 0.29215529928918754, - 0.2623466604550623, - 0.23834483686513633, - 0.22243107112974694, - 0.1995573966568698, - 0.16866181603372785, - 0.14156508223446862, - 0.1310547562966207, - 0.10229517184146873, - 0.07875529691231123, - 0.06135097009300107, - 0.04763420902556625 + 0.9993171743502156, + 0.9891133604383114, + 0.9794774970508517, + 0.9502040774996521, + 0.9060341324769974, + 0.8334251677917976, + 0.7771168689710242, + 0.6974021053118046, + 0.6339153972684118, + 0.5915784484997256, + 0.5322031930524332, + 0.4483792206958328, + 0.3781738507181198, + 0.34870522080743893, + 0.27171585028807743, + 0.21063428750487176, + 0.16400709022665244, + 0.12754291142997942 ] }, "esophagus cont": { @@ -239,24 +239,24 @@ "f": 0.31999999999999995, "Dp": 0.030000000000000002, "data": [ - 0.3758855286172819, - 0.37196297068833584, - 0.3677486036668563, - 0.3570514580866963, - 0.3400711095127909, - 0.31262201594188704, - 0.29142290332076964, - 0.261925997464044, - 0.23931515460210578, - 0.22207697583074673, - 0.20034975290371432, - 0.16804761249126085, - 0.1419008635732186, - 0.1311290113297171, - 0.10146448479190706, - 0.07934001282398631, - 0.062194341247799524, - 0.048487144784195864 + 1.0001332280689843, + 0.9895985875899938, + 0.9789478029216182, + 0.9499445641099479, + 0.9055147553106474, + 0.8327969031957817, + 0.7763844730026062, + 0.6969814423207864, + 0.6348857150053814, + 0.5912243532007254, + 0.5329955492992777, + 0.4477650171533658, + 0.37850963205686977, + 0.34877947584053537, + 0.27088516323851575, + 0.21121900341654684, + 0.1648504613814509, + 0.12839584718860902 ] }, "st wall": { @@ -265,24 +265,24 @@ "f": 0.3, "Dp": 0.012000000000000002, "data": [ - 0.3101379786693945, - 0.3083163155914283, - 0.3080219178648329, - 0.3030154031125323, - 0.2968650406573065, - 0.28444479207220924, - 0.27335281402354256, - 0.2531421585479966, - 0.23190929758794723, - 0.21470347820008495, - 0.18828823156024074, - 0.1535095728179908, - 0.12953859434718284, - 0.12005568022121892, - 0.09507658543806999, - 0.07681041851276213, - 0.06138391911456677, - 0.04817672734560116 + 0.9998513623271699, + 0.9948379132892078, + 0.9913822548339422, + 0.9770716021779204, + 0.9559927316920448, + 0.9157396120124381, + 0.8792668044636494, + 0.8146129470898368, + 0.747462493232909, + 0.6925740494438698, + 0.608014014415594, + 0.4956340448525544, + 0.4182439457406493, + 0.3867244415911866, + 0.3069376422938969, + 0.24580667102000056, + 0.1963007051879767, + 0.15590509909570116 ] }, "Stomach Contents": { @@ -291,24 +291,24 @@ "f": 0.0, "Dp": 0.0, "data": [ - 0.5126018871088376, - 0.5110596279871825, - 0.5093535694210771, - 0.5046118029961769, - 0.4975235052032258, - 0.4831126643032834, - 0.4685144470320901, - 0.44098858155273923, - 0.4083164396340143, - 0.3801538814981812, - 0.32617856922898014, - 0.24204450859420612, - 0.17942509249683888, - 0.15492912843811152, - 0.09842158158269289, - 0.06316964601772247, - 0.04009111436010544, - 0.02635011387457495 + 1.0000580074394811, + 0.9970555713174671, + 0.9938937097177735, + 0.9848106471664809, + 0.9705731199789829, + 0.9421815501092592, + 0.9140157968535895, + 0.8605459524785368, + 0.7975580576515555, + 0.7412702572219417, + 0.636994314232129, + 0.4723024757673014, + 0.35000439003580075, + 0.30174809044287926, + 0.19203748494882025, + 0.12286178144346882, + 0.07815250033798066, + 0.05061912506381041 ] }, "pancreas": { @@ -317,24 +317,24 @@ "f": 0.14999999999999997, "Dp": 0.009999999999999998, "data": [ - 0.38820347726551635, - 0.38671855752043993, - 0.38597535823658624, - 0.3823051985581999, - 0.37752939060122326, - 0.36813891274934296, - 0.35975046078101547, - 0.34452128623453676, - 0.3256473272848762, - 0.31050247244569923, - 0.283784020243701, - 0.2435621256337855, - 0.21177168118302228, - 0.19756934627873432, - 0.16211144416180834, - 0.13295914534689968, - 0.10879080126869926, - 0.09020835794778942 + 1.0003875681734176, + 0.9973129244965385, + 0.9949899710080956, + 0.9866394555521574, + 0.9742540746981484, + 0.9503225789260812, + 0.9282312411494005, + 0.8878266735221373, + 0.8410401995615366, + 0.8012066087764987, + 0.7324408744234978, + 0.6270715836463917, + 0.5446837444544892, + 0.5086138456975294, + 0.41704100663392957, + 0.3424989685263882, + 0.2811572132009703, + 0.23202621068272192 ] }, "Right kydney cortex": { @@ -343,24 +343,24 @@ "f": 0.09699999999999999, "Dp": 0.019999999999999997, "data": [ - 0.5021735733308593, - 0.5001897051856058, - 0.4977519367369546, - 0.49233614253361235, - 0.4838451608236118, - 0.46750362571995796, - 0.45255769135060814, - 0.42502787545804394, - 0.3969183769732045, - 0.373248902416415, - 0.33355286509783577, - 0.26747267793394397, - 0.21551936575605565, - 0.19433815539241997, - 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"Vein": true + "Blood RV": true }, "options": { "thresholds": [500]