diff --git a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py index 6934e014..772744e4 100644 --- a/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py +++ b/phantoms/MR_XCAT_qMRI/sim_ivim_sig.py @@ -451,8 +451,10 @@ def parse_bvalues_file(file_path): voxel_selector_fraction = 0.5 D, f, Ds = contrast_curve_calc() - ignore = np.isnan(D) + ignore = np.logical_or(np.logical_or(np.isnan(D),f<0.03),f>0.97) generic_data = {} + seen_combinations = set() + for level, name in legend.items(): if len(ignore) > level and ignore[level]: continue @@ -460,6 +462,18 @@ def parse_bvalues_file(file_path): voxels = sig[selector] if len(voxels) < 1: continue + D_val = np.median(Dim[selector], axis=0) + f_val = np.median(fim[selector], axis=0) + Dp_val = np.median(Dpim[selector], axis=0) + + combo = (tuple(np.atleast_1d(D_val)), + tuple(np.atleast_1d(f_val)), + tuple(np.atleast_1d(Dp_val))) + + if combo in seen_combinations: + continue + + seen_combinations.add(combo) signals = np.squeeze(voxels[int(voxels.shape[0] * voxel_selector_fraction)]).tolist() generic_data[name] = { 'noise': noise, diff --git a/tests/IVIMmodels/unit_tests/generic.json b/tests/IVIMmodels/unit_tests/generic.json index c1e2477b..fc70018a 100644 --- a/tests/IVIMmodels/unit_tests/generic.json +++ b/tests/IVIMmodels/unit_tests/generic.json @@ -25,32 +25,6 @@ 0.07638861567746785 ] }, - "myocardium RV": { - "noise": 0.0005, - "D": 0.0024, - "f": 0.15, - "Dp": 0.08, - "data": [ - 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": { "noise": 0.0005, "D": 0.0015, @@ -77,58 +51,6 @@ 0.2068495366721375 ] }, - "Blood RV": { - "noise": 0.0005, - "D": 0.003, - "f": 1.0, - "Dp": 0.1, - "data": [ - 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, - -3.057038566732644e-05 - ] - }, - "Blood RA": { - "noise": 0.0005, - "D": 0.003, - "f": 1.0, - "Dp": 0.1, - "data": [ - 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, - 5.962153441482305e-05 - ] - }, "muscle": { "noise": 0.0005, "D": 0.00137, @@ -181,32 +103,6 @@ 0.19882602755160078 ] }, - "gall bladder": { - "noise": 0.0005, - "D": 0.003, - "f": 0.0, - "Dp": 0.1, - "data": [ - 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": { "noise": 0.0005, "D": 0.00167, @@ -233,32 +129,6 @@ 0.12754291142997942 ] }, - "esophagus cont": { - "noise": 0.0005, - "D": 0.00167, - "f": 0.32, - "Dp": 0.03, - "data": [ - 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": { "noise": 0.0005, "D": 0.0015, @@ -285,32 +155,6 @@ 0.15590509909570116 ] }, - "Stomach Contents": { - "noise": 0.0005, - "D": 0.003, - "f": 0.0, - "Dp": 0.0, - "data": [ - 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": { "noise": 0.0005, "D": 0.0013, @@ -389,58 +233,6 @@ 0.10356078464838264 ] }, - "Left kidney cortex": { - "noise": 0.0005, - "D": 0.00212, - "f": 0.097, - "Dp": 0.02, - "data": [ - 1.0011945854174855, - 0.9955396602100857, - 0.9918214155056828, - 0.9812684164210659, - 0.963098747825943, - 0.930912664496857, - 0.9000687778422743, - 0.8484119945257521, - 0.7920259614209312, - 0.7434277758611111, - 0.6614289565458207, - 0.5323474665735095, - 0.4293903595942227, - 0.38651481842000707, - 0.2821716436119705, - 0.20476916115368815, - 0.14953578190775682, - 0.1076376696836249 - ] - }, - "left kidney medulla": { - "noise": 0.0005, - "D": 0.00209, - "f": 0.158, - "Dp": 0.019, - "data": [ - 0.999784883468332, - 0.9956275637829168, - 0.9897288582217845, - 0.9772893183868882, - 0.9566347399935364, - 0.9148307724225175, - 0.8794381537213443, - 0.8201110314907877, - 0.7567369118787439, - 0.7062127395964859, - 0.625573903050984, - 0.5012834077932828, - 0.4049049660412132, - 0.3642551567909775, - 0.2671478449807342, - 0.1948282799148607, - 0.14272699354254856, - 0.10447427993309061 - ] - }, "spleen": { "noise": 0.0005, "D": 0.0013, @@ -519,58 +311,6 @@ 0.5563023125518155 ] }, - "Artery": { - "noise": 0.0005, - "D": 0.003, - "f": 1.0, - "Dp": 0.1, - "data": [ - 0.9997800501422142, - 0.9045819629490028, - 0.818088444799732, - 0.6062531634694728, - 0.36835081010301113, - 0.13565643887731554, - 0.04941515572602334, - 0.006047036365649863, - 0.000358653575991588, - -0.00032459849416059477, - -0.0007608227498529157, - 5.1438393887969995e-05, - 0.00019454498032650262, - -6.96219775034424e-05, - 0.0004213480781055518, - -0.0007729334158231029, - -0.0002834467902361242, - 0.00037229679238038097 - ] - }, - "Vein": { - "noise": 0.0005, - "D": 0.003, - "f": 1.0, - "Dp": 0.1, - "data": [ - 1.0001149665130338, - 0.9052158548961062, - 0.8192496016137271, - 0.6069001173171487, - 0.36753116759462695, - 0.13519606730978775, - 0.04965233826725912, - 0.006764269797673213, - 0.00030705658106631984, - 6.365223281603042e-05, - -7.519056957567633e-05, - -3.61461581814404e-05, - 3.0156761329221312e-05, - -0.0003928484200171012, - 0.0004656170878741209, - -9.935576265301419e-05, - -0.00013896810647857585, - 0.00022133391960194875 - ] - }, "asc lower intestine": { "noise": 0.0005, "D": 0.00131, @@ -597,84 +337,6 @@ 0.08487549935755932 ] }, - "trans lower intestine": { - "noise": 0.0005, - "D": 0.00131, - "f": 0.69, - "Dp": 0.029, - "data": [ - 0.9997303817205065, - 0.9794580744935948, - 0.9604711875831552, - 0.9050086591438171, - 0.8218151851876994, - 0.6890179954687737, - 0.5865846418363266, - 0.4519190479283628, - 0.36000260876813217, - 0.31008144191779136, - 0.26376048077496717, - 0.223671979602434, - 0.1960893389844811, - 0.1838359226391205, - 0.15162732015321162, - 0.12426136226164565, - 0.10201646999685307, - 0.08268553179392053 - ] - }, - "desc lower intestine": { - "noise": 0.0005, - "D": 0.00131, - "f": 0.69, - "Dp": 0.029, - "data": [ - 0.9998169952297454, - 0.9794581567785913, - 0.9611748946566195, - 0.90458376353294, - 0.8222853652765572, - 0.6884864031834491, - 0.5867353229852139, - 0.45199611132761436, - 0.3592817956229402, - 0.30944572861898323, - 0.2628024541204303, - 0.2236254487524024, - 0.19613360547699618, - 0.18238665571578985, - 0.15066862880035628, - 0.12406987012052711, - 0.10222792937336041, - 0.08376298023754827 - ] - }, - "small intestine": { - "noise": 0.0005, - "D": 0.00131, - "f": 0.69, - "Dp": 0.029, - "data": [ - 1.000672478806307, - 0.9801710601503958, - 0.9609114603189408, - 0.9038640653485989, - 0.8217913958709209, - 0.6874638577111291, - 0.5873916251429048, - 0.45172009389536083, - 0.35931580081980474, - 0.3102674128607682, - 0.263445124824966, - 0.22333874634028628, - 0.19514824524892244, - 0.18379440735891486, - 0.15068757445687012, - 0.12373605827586043, - 0.10115024125349835, - 0.08396227376915624 - ] - }, "pericardium": { "noise": 0.0005, "D": 0.003, diff --git a/tests/IVIMmodels/unit_tests/generic_DL.json b/tests/IVIMmodels/unit_tests/generic_DL.json index 46fd4944..106eac9c 100644 --- a/tests/IVIMmodels/unit_tests/generic_DL.json +++ b/tests/IVIMmodels/unit_tests/generic_DL.json @@ -5,54 +5,24 @@ "f": 0.15, "Dp": 0.08, "data": [ - 1.033180924902301, - 0.9607468657793776, - 0.912606451182656, - 0.888620393895259, - 0.8418819322382458, - 0.884731423360733, - 0.8948278336097781, - 0.8166950158442055, - 0.6786227776445861, - 0.6874715517646282, - 0.6056532504758427, - 0.47986924885264165, - 0.41929421834511005, - 0.37360032607203914, - 0.28445075605440917, - 0.1282091905031671, - 0.07311015923259691, - 0.0856679032303328, - 0.042585284457289964, - 0.0033612521618336458 - ] - }, - "myocardium RV": { - "noise": 0.04, - "D": 0.0024, - "f": 0.15, - "Dp": 0.08, - "data": [ - 1.0145043798675288, - 0.9660196612863166, - 0.8867224861101718, - 0.91705752667823, - 0.8595526518110584, - 0.8017899336155123, - 0.7550511551970039, - 0.8086809241124706, - 0.688194063129757, - 0.6299522963355337, - 0.5469383807534097, - 0.4608083021236803, - 0.41392592502242126, - 0.37413426739765343, - 0.16685997968777203, - 0.20901258338016387, - 0.09652919594429378, - 0.05426096728953708, - 0.06155920372827745, - 0.03188929035836821 + 1.0098540139680026, + 0.9826939123364847, + 0.9680070551127059, + 0.9051951923775081, + 0.8558712574646193, + 0.8420463802228705, + 0.8405679561261958, + 0.7634791085579523, + 0.6918665709339131, + 0.6147515040309017, + 0.5785075121314839, + 0.4553468940020642, + 0.37626344938607714, + 0.328749789527815, + 0.2116297275844832, + 0.21399002904014153, + 0.18214686306523659, + 0.01937869081337886 ] }, "myocardium ra": { @@ -61,82 +31,24 @@ "f": 0.07, "Dp": 0.07, "data": [ - 1.0092083343835259, - 0.9661574802430908, - 0.990206450003812, - 0.9706325316312445, - 0.9767925839190637, - 0.9220420032510354, - 0.896704422240442, - 0.8176423934101318, - 0.7947310478273071, - 0.8513319609173063, - 0.717433034543031, - 0.6668879161875433, - 0.5076708740135724, - 0.41907282532720147, - 0.46365437068395976, - 0.3304714439286537, - 0.23296693987075087, - 0.23487193869963477, - 0.15137581352968732, - 0.19376654820017183 - ] - }, - "Blood RV": { - "noise": 0.04, - "D": 0.003, - "f": 1.0, - "Dp": 0.1, - "data": [ - 1.0032938194881618, - 0.9011074959881675, - 0.8247177241346322, - 0.6217936665654985, - 0.36359185175179465, - 0.10916941666421531, - 0.07514868579091256, - -0.007457187020223218, - -0.015334743664598449, - 0.035584748512989074, - -0.06094237055801714, - 0.02686274837179178, - 0.017606840455411082, - -0.06800439631952913, - -0.0021446239806577104, - -0.04652851137385713, - 0.007809266022958561, - 0.004337716720120069, - -0.022322891625288062, - -0.008937096639451064 - ] - }, - "Blood RA": { - "noise": 0.04, - "D": 0.003, - "f": 1.0, - "Dp": 0.1, - "data": [ - 1.0391432255942619, - 0.8937085668773437, - 0.8561831176249705, - 0.5766637377982473, - 0.32798363085925153, - 0.11937274238334296, - 0.006607428437157149, - 0.041804062920864915, - 0.07147779149049599, - 0.03153301989127758, - -0.02089298817635404, - 0.04708131846092277, - 0.02742898143058931, - 0.022164981689256565, - -0.019016312292452823, - -0.02353957465336293, - 0.024688437266257503, - 0.012942951338985542, - 0.044936193924032856, - 0.048828299443163144 + 1.0406717995505752, + 0.9501960180486319, + 1.053868272098131, + 0.9679990715927623, + 1.0053632512411972, + 0.8836365944117994, + 0.9230502523164995, + 0.8765208001873821, + 0.8064797376133074, + 0.7736466352849087, + 0.6856536025758, + 0.7091736978193912, + 0.4342890792845645, + 0.4836751055688441, + 0.4511202880668142, + 0.23151897852233178, + 0.26413406887522073, + 0.15459006766586506 ] }, "muscle": { @@ -145,26 +57,24 @@ "f": 0.1, "Dp": 0.0263, "data": [ - 0.9771421455163913, - 0.9834454308259023, - 0.9452156251065997, - 1.0044139802947745, - 0.915969921803736, - 0.9422614234128238, - 0.966768746315094, - 0.8868649011898158, - 0.801775641750857, - 0.7421732033410118, - 0.7197688278589072, - 0.6313747309126961, - 0.5570672087225664, - 0.5099772094974028, - 0.4049154491880213, - 0.2851134303775019, - 0.23608983440436468, - 0.2236446560863158, - 0.17276532513782425, - 0.1590053575168229 + 1.002603033075884, + 0.9697360475077582, + 0.9795040118515252, + 0.9144040832910203, + 1.0115515328731417, + 0.9544652319614496, + 0.9182601488335194, + 0.8127574832669384, + 0.8739770272527798, + 0.8467281293101417, + 0.7173371036356685, + 0.6185480801480356, + 0.5095700458236414, + 0.48659301101208124, + 0.505469597106218, + 0.3033780704919908, + 0.2628760533454496, + 0.18774252312454337 ] }, "Liver": { @@ -173,54 +83,24 @@ "f": 0.11, "Dp": 0.1, "data": [ - 1.0045581555314624, - 1.0213638998197319, - 0.969398694488538, - 0.9838565535209267, - 0.9501015461451721, - 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