I am trying to create a mesh of finite elements of a medical image, I pass that format to Gmsh and then read it in FreeFem++ but I have a mistake, could you help me how to create this mesh with FreeFem, please.
This is my code:
//mesh unstructured version ACSII-2
//Rodar no terminal:
//gmsh -2 -format msh2 -string ‘Mesh.SaveElementTagType=2;’ mama.geo
load “gmsh”
mesh sq = gmshload(“mama.msh”);
plot(sq, wait = true, cmm=“Exportando_malha_Gmsh”);
The Gmsh file:
//
lc1 = 5;
Point(1) = { 177.000000 , 252.478937 ,0 , lc1 };
Point(2) = { 177.510050 , 254.000000 ,0 , lc1 };
Point(3) = { 178.000000 , 255.488332 ,0 , lc1 };
Point(4) = { 178.503309 , 257.000000 ,0 , lc1 };
Point(5) = { 179.000000 , 258.488197 ,0 , lc1 };
Point(6) = { 179.715569 , 260.000000 ,0 , lc1 };
Point(7) = { 180.270890 , 261.000000 ,0 , lc1 };
Point(8) = { 180.724259 , 263.000000 ,0 , lc1 };
Point(9) = { 181.279331 , 264.000000 ,0 , lc1 };
Point(10) = { 182.000000 , 265.515699 ,0 , lc1 };
Point(11) = { 182.701592 , 267.000000 ,0 , lc1 };
Point(12) = { 183.274872 , 268.000000 ,0 , lc1 };
Point(13) = { 184.000000 , 269.520736 ,0 , lc1 };
Point(14) = { 184.700018 , 271.000000 ,0 , lc1 };
Point(15) = { 185.480041 , 272.000000 ,0 , lc1 };
Point(16) = { 186.270932 , 273.000000 ,0 , lc1 };
Point(17) = { 187.000000 , 274.523458 ,0 , lc1 };
Point(18) = { 187.703792 , 276.000000 ,0 , lc1 };
Point(19) = { 188.278432 , 277.000000 ,0 , lc1 };
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Point(25) = { 192.488638 , 285.000000 ,0 , lc1 };
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Point(29) = { 195.273466 , 290.000000 ,0 , lc1 };
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Point(65) = { 220.513692 , 337.000000 ,0 , lc1 };
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Line(1) = {1,2};
Line(2) = {2,3};
Line(3) = {3,4};
Line(4) = {4,5};
Line(5) = {5,6};
Line(6) = {6,7};
Line(7) = {7,8};
Line(8) = {8,9};
Line(9) = {9,10};
Line(10) = {10,11};
Line(11) = {11,12};
Line(12) = {12,13};
Line(13) = {13,14};
Line(14) = {14,15};
Line(15) = {15,16};
Line(16) = {16,17};
Line(17) = {17,18};
Line(18) = {18,19};
Line(19) = {19,20};
Line(20) = {20,21};
Line(21) = {21,22};
Line(22) = {22,23};
Line(23) = {23,24};
Line(24) = {24,25};
Line(25) = {25,26};
Line(26) = {26,27};
Line(27) = {27,28};
Line(28) = {28,29};
Line(29) = {29,30};
Line(30) = {30,31};
Line(31) = {31,32};
Line(32) = {32,33};
Line(33) = {33,34};
Line(34) = {34,35};
Line(35) = {35,36};
Line(36) = {36,37};
Line(37) = {37,38};
Line(38) = {38,39};
Line(39) = {39,40};
Line(40) = {40,41};
Line(41) = {41,42};
Line(42) = {42,43};
Line(43) = {43,44};
Line(44) = {44,45};
Line(45) = {45,46};
Line(46) = {46,47};
Line(47) = {47,48};
Line(48) = {48,49};
Line(49) = {49,50};
Line(50) = {50,51};
Line(51) = {51,52};
Line(52) = {52,53};
Line(53) = {53,54};
Line(54) = {54,55};
Line(55) = {55,56};
Line(56) = {56,57};
Line(57) = {57,58};
Line(58) = {58,59};
Line(59) = {59,60};
Line(60) = {60,61};
Line(61) = {61,62};
Line(62) = {62,63};
Line(63) = {63,64};
Line(64) = {64,65};
Line(65) = {65,66};
Line(66) = {66,67};
Line(67) = {67,68};
Line(68) = {68,69};
Line(69) = {69,70};
Line(70) = {70,71};
Line(71) = {71,72};
Line(72) = {72,73};
Line(73) = {73,74};
Line(74) = {74,75};
Line(75) = {75,76};
Line(76) = {76,77};
Line(77) = {77,78};
Line(78) = {78,79};
Line(79) = {79,80};
Line(80) = {80,81};
Line(81) = {81,82};
Line(82) = {82,83};
Line(83) = {83,84};
Line(84) = {84,85};
Line(85) = {85,86};
Line(86) = {86,87};
Line(87) = {87,88};
Line(88) = {88,89};
Line(89) = {89,90};
Line(90) = {90,91};
Line(91) = {91,92};
Line(92) = {92,93};
Line(93) = {93,94};
Line(94) = {94,95};
Line(95) = {95,96};
Line(96) = {96,97};
Line(97) = {97,98};
Line(98) = {98,99};
Line(99) = {99,100};
Line(100) = {100,101};
Line(101) = {101,102};
Line(102) = {102,103};
Line(103) = {103,104};
Line(104) = {104,105};
Line(105) = {105,106};
Line(106) = {106,107};
Line(107) = {107,108};
Line(108) = {108,109};
Line(109) = {109,110};
Line(110) = {110,111};
Line(111) = {111,112};
Line(112) = {112,113};
Line(113) = {113,114};
Line(114) = {114,115};
Line(115) = {115,116};
Line(116) = {116,117};
Line(117) = {117,118};
Line(118) = {118,119};
Line(119) = {119,120};
Line(120) = {120,121};
Line(121) = {121,122};
Line(122) = {122,123};
Line(123) = {123,124};
Line(124) = {124,125};
Line(125) = {125,126};
Line(126) = {126,127};
Line(127) = {127,128};
Line(128) = {128,129};
Line(129) = {129,130};
Line(130) = {130,131};
Line(131) = {131,132};
Line(132) = {132,133};
Line(133) = {133,134};
Line(134) = {134,135};
Line(135) = {135,136};
Line(136) = {136,137};
Line(137) = {137,138};
Line(138) = {138,139};
Line(139) = {139,140};
Line(140) = {140,141};
Line(141) = {141,142};
Line(142) = {142,143};
Line(143) = {143,144};
Line(144) = {144,145};
Line(145) = {145,146};
Line(146) = {146,147};
Line(147) = {147,148};
Line(148) = {148,149};
Line(149) = {149,150};
Line(150) = {150,151};
Line(151) = {151,152};
Line(152) = {152,153};
Line(153) = {153,154};
Line(154) = {154,155};
Line(155) = {155,156};
Line(156) = {156,157};
Line(157) = {157,158};
Line(158) = {158,159};
Line(159) = {159,160};
Line(160) = {160,161};
Line(161) = {161,162};
Line(162) = {162,163};
Line(163) = {163,164};
Line(164) = {164,165};
Line(165) = {165,166};
Line(166) = {166,167};
Line(167) = {167,168};
Line(168) = {168,169};
Line(169) = {169,170};
Line(170) = {170,171};
Line(171) = {171,172};
Line(172) = {172,173};
Line(173) = {173,174};
Line(174) = {174,175};
Line(175) = {175,176};
Line(176) = {176,177};
Line(177) = {177,178};
Line(178) = {178,179};
Line(179) = {179,180};
Line(180) = {180,181};
Line(181) = {181,182};
Line(182) = {182,183};
Line(183) = {183,184};
Line(184) = {184,185};
Line(185) = {185,186};
Line(186) = {186,187};
Line(187) = {187,188};
Line(188) = {188,189};
Line(189) = {189,190};
Line(190) = {190,191};
Line(191) = {191,192};
Line(192) = {192,193};
Line(193) = {193,194};
Line(194) = {194,195};
Line(195) = {195,196};
Line(196) = {196,197};
Line(197) = {197,198};
Line(198) = {198,199};
Line(199) = {199,200};
Line(200) = {200,201};
Line(201) = {201,202};
Line(202) = {202,203};
Line(203) = {203,204};
Line(204) = {204,205};
Line(205) = {205,206};
Line(206) = {206,207};
Line(207) = {207,208};
Line(208) = {208,209};
Line(209) = {209,210};
Line(210) = {210,211};
Line(211) = {211,212};
Line(212) = {212,213};
Line(213) = {213,214};
Line(214) = {214,215};
Line(215) = {215,216};
Line(216) = {216,217};
Line(217) = {217,218};
Line(218) = {218,219};
Line(219) = {219,220};
Line(220) = {220,221};
Line(221) = {221,222};
Line(222) = {222,223};
Line(223) = {223,224};
Line(224) = {224,225};
Line(225) = {225,226};
Line(226) = {226,227};
Line(227) = {227,228};
Line(228) = {228,229};
Line(229) = {229,230};
Line(230) = {230,231};
Line(231) = {231,232};
Line(232) = {232,233};
Line(233) = {233,234};
Line(234) = {234,235};
Line(235) = {235,236};
Line(236) = {236,237};
Line(237) = {237,238};
Line(238) = {238,239};
Line(239) = {239,240};
Line(240) = {240,241};
Line(241) = {241,242};
Line(242) = {242,243};
Line(243) = {243,244};
Line(244) = {244,245};
Line(245) = {245,246};
Line(246) = {246,247};
Line(247) = {247,248};
Line(248) = {248,249};
Line(249) = {249,250};
Line(250) = {250,251};
Line(251) = {251,252};
Line(252) = {252,253};
Line(253) = {253,254};
Line(254) = {254,255};
Line(255) = {255,256};
Line(256) = {256,257};
Line(257) = {257,258};
Line(258) = {258,259};
Line(259) = {259,260};
Line(260) = {260,261};
Line(261) = {261,262};
Line(262) = {262,263};
Line(263) = {263,264};
Line(264) = {264,265};
Line(265) = {265,266};
Line(266) = {266,267};
Line(267) = {267,268};
Line(268) = {268,269};
Line(269) = {269,270};
Line(270) = {270,271};
Line(271) = {271,272};
Line(272) = {272,273};
Line(273) = {273,274};
Line(274) = {274,275};
Line(275) = {275,276};
Line(276) = {276,277};
Line(277) = {277,278};
Line(278) = {278,279};
Line(279) = {279,280};
Line(280) = {280,281};
Line(281) = {281,282};
Line(282) = {282,283};
Line(283) = {283,284};
Line(284) = {284,285};
Line(285) = {285,286};
Line(286) = {286,287};
Line(287) = {287,288};
Line(288) = {288,289};
Line(289) = {289,290};
Line(290) = {290,291};
Line(291) = {291,292};
Line(292) = {292,293};
Line(293) = {293,294};
Line(294) = {294,295};
Line(295) = {295,296};
Line(296) = {296,297};
Line(297) = {297,298};
Line(298) = {298,299};
Line(299) = {299,300};
Line(300) = {300,301};
Line(301) = {301,302};
Line(302) = {302,303};
Line(303) = {303,304};
Line(304) = {304,305};
Line(305) = {305,306};
Line(306) = {306,307};
Line(307) = {307,308};
Line(308) = {308,309};
Line(309) = {309,310};
Line(310) = {310,311};
Line(311) = {311,312};
Line(312) = {312,313};
Line(313) = {313,314};
Line(314) = {314,315};
Line(315) = {315,316};
Line(316) = {316,317};
Line(317) = {317,318};
Line(318) = {318,319};
Line(319) = {319,320};
Line(320) = {320,1};
Line Loop(1) = {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320};
Plane Surface(2) = {1};
Physical Surface(99) = {2};
//Physical Line(1) = {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320};
The erro:
current line = 8
Assertion fail : (area > 0)
line :301, in file ./include/fem.hpp
Assertion fail : (area > 0)
line :301, in file ./include/fem.hpp
err code 6 , mpirank 0