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reg.align_maps() stuck in the middle, won't complete the process #2

Closed nuwanarti closed 4 years ago

nuwanarti commented 4 years ago

Looks like reg.align_maps() won't complete the process. here is the output, but it doesn't complete the process

========================================================================

Eigenvector Sorting Results

========================================================================
The matches for eigenvectors were as follows:
Target  |  Source
     0  |  0     
     1  |  1     
     2  |  2     
     3  |  3     
     4  |  4     
     5  |  5     
*Negative source values means those eigenvectors were flipped*

Number of features (including spectral) used for registartion: 3
========================================================================

Non-Rigid (Deformable) Registration Beginning

========================================================================
Iteration:1
ML: -8389.450;  ML change (error):  8389.450;   Sigma^2:     0.069;     Sigma^2 change:     0.106
[                                                                        ]
Iteration:2
ML: -9115.060;  ML change (error):   725.610;   Sigma^2:     0.060;     Sigma^2 change:     0.009
[                                                                        ]
Iteration:3
ML: -9167.780;  ML change (error):    52.720;   Sigma^2:     0.051;     Sigma^2 change:     0.009
[                                                                        ]
Iteration:4
ML: -9236.975;  ML change (error):    69.195;   Sigma^2:     0.042;     Sigma^2 change:     0.010
[                                                                        ]
Iteration:5
ML: -9338.161;  ML change (error):   101.186;   Sigma^2:     0.032;     Sigma^2 change:     0.010
[=                                                                       ]
Iteration:6
ML: -9477.696;  ML change (error):   139.535;   Sigma^2:     0.023;     Sigma^2 change:     0.009
[=                                                                       ]
Iteration:7
ML: -9641.891;  ML change (error):   164.195;   Sigma^2:     0.016;     Sigma^2 change:     0.007
[=                                                                       ]
Iteration:8
ML: -9814.003;  ML change (error):   172.112;   Sigma^2:     0.011;     Sigma^2 change:     0.005
[=                                                                       ]
Iteration:9
ML: -9986.759;  ML change (error):   172.756;   Sigma^2:     0.008;     Sigma^2 change:     0.003
[==                                                                      ]
Iteration:10
ML:-10157.358;  ML change (error):   170.599;   Sigma^2:     0.006;     Sigma^2 change:     0.002
[==                                                                      ]
Iteration:11
ML:-10323.423;  ML change (error):   166.066;   Sigma^2:     0.004;     Sigma^2 change:     0.002
[==                                                                      ]
Iteration:12
ML:-10482.716;  ML change (error):   159.293;   Sigma^2:     0.003;     Sigma^2 change:     0.001
[==                                                                      ]
Iteration:13
ML:-10632.643;  ML change (error):   149.927;   Sigma^2:     0.002;     Sigma^2 change:     0.001
[===                                                                     ]
Iteration:14
ML:-10769.638;  ML change (error):   136.995;   Sigma^2:     0.001;     Sigma^2 change:     0.001
[===                                                                     ]
Iteration:15
ML:-10889.379;  ML change (error):   119.741;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===                                                                     ]
Iteration:16
ML:-10986.901;  ML change (error):    97.523;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===                                                                     ]
Iteration:17
ML:-11058.007;  ML change (error):    71.105;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====                                                                    ]
Iteration:18
ML:-11102.755;  ML change (error):    44.749;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====                                                                    ]
Iteration:19
ML:-11126.791;  ML change (error):    24.036;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====                                                                    ]
Iteration:20
ML:-11138.080;  ML change (error):    11.289;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====                                                                    ]
Iteration:21
ML:-11142.988;  ML change (error):     4.908;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====                                                                   ]
Iteration:22
ML:-11145.126;  ML change (error):     2.138;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====                                                                   ]
Iteration:23
ML:-11146.143;  ML change (error):     1.017;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====                                                                   ]
Iteration:24
ML:-11146.705;  ML change (error):     0.562;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====                                                                   ]
Iteration:25
ML:-11147.070;  ML change (error):     0.364;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======                                                                  ]
Iteration:26
ML:-11147.336;  ML change (error):     0.267;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======                                                                  ]
Iteration:27
ML:-11147.548;  ML change (error):     0.212;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======                                                                  ]
Iteration:28
ML:-11147.725;  ML change (error):     0.177;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======                                                                  ]
Iteration:29
ML:-11147.877;  ML change (error):     0.153;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======                                                                  ]
Iteration:30
ML:-11148.012;  ML change (error):     0.135;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======                                                                 ]
Iteration:31
ML:-11148.134;  ML change (error):     0.122;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======                                                                 ]
Iteration:32
ML:-11148.245;  ML change (error):     0.111;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======                                                                 ]
Iteration:33
ML:-11148.348;  ML change (error):     0.103;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======                                                                 ]
Iteration:34
ML:-11148.443;  ML change (error):     0.096;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========                                                                ]
Iteration:35
ML:-11148.534;  ML change (error):     0.090;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========                                                                ]
Iteration:36
ML:-11148.619;  ML change (error):     0.085;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========                                                                ]
Iteration:37
ML:-11148.701;  ML change (error):     0.081;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========                                                                ]
Iteration:38
ML:-11148.778;  ML change (error):     0.078;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========                                                               ]
Iteration:39
ML:-11148.853;  ML change (error):     0.074;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========                                                               ]
Iteration:40
ML:-11148.924;  ML change (error):     0.071;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========                                                               ]
Iteration:41
ML:-11148.992;  ML change (error):     0.068;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========                                                               ]
Iteration:42
ML:-11149.058;  ML change (error):     0.066;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========                                                              ]
Iteration:43
ML:-11149.121;  ML change (error):     0.063;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========                                                              ]
Iteration:44
ML:-11149.181;  ML change (error):     0.061;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========                                                              ]
Iteration:45
ML:-11149.239;  ML change (error):     0.058;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========                                                              ]
Iteration:46
ML:-11149.295;  ML change (error):     0.056;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========                                                             ]
Iteration:47
ML:-11149.348;  ML change (error):     0.053;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========                                                             ]
Iteration:48
ML:-11149.399;  ML change (error):     0.051;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========                                                             ]
Iteration:49
ML:-11149.447;  ML change (error):     0.048;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========                                                             ]
Iteration:50
ML:-11149.494;  ML change (error):     0.046;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============                                                            ]
Iteration:51
ML:-11149.537;  ML change (error):     0.044;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============                                                            ]
Iteration:52
ML:-11149.579;  ML change (error):     0.042;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============                                                            ]
Iteration:53
ML:-11149.619;  ML change (error):     0.039;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============                                                            ]
Iteration:54
ML:-11149.656;  ML change (error):     0.037;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============                                                            ]
Iteration:55
ML:-11149.691;  ML change (error):     0.035;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============                                                           ]
Iteration:56
ML:-11149.724;  ML change (error):     0.033;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============                                                           ]
Iteration:57
ML:-11149.756;  ML change (error):     0.031;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============                                                           ]
Iteration:58
ML:-11149.785;  ML change (error):     0.029;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============                                                           ]
Iteration:59
ML:-11149.813;  ML change (error):     0.028;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============                                                          ]
Iteration:60
ML:-11149.839;  ML change (error):     0.026;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============                                                          ]
Iteration:61
ML:-11149.863;  ML change (error):     0.024;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============                                                          ]
Iteration:62
ML:-11149.886;  ML change (error):     0.023;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============                                                          ]
Iteration:63
ML:-11149.907;  ML change (error):     0.021;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============                                                         ]
Iteration:64
ML:-11149.927;  ML change (error):     0.020;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============                                                         ]
Iteration:65
ML:-11149.945;  ML change (error):     0.018;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============                                                         ]
Iteration:66
ML:-11149.962;  ML change (error):     0.017;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============                                                         ]
Iteration:67
ML:-11149.978;  ML change (error):     0.016;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================                                                        ]
Iteration:68
ML:-11149.993;  ML change (error):     0.015;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================                                                        ]
Iteration:69
ML:-11150.007;  ML change (error):     0.014;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================                                                        ]
Iteration:70
ML:-11150.020;  ML change (error):     0.013;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================                                                        ]
Iteration:71
ML:-11150.032;  ML change (error):     0.012;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================                                                       ]
Iteration:72
ML:-11150.043;  ML change (error):     0.011;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================                                                       ]
Iteration:73
ML:-11150.053;  ML change (error):     0.010;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================                                                       ]
Iteration:74
ML:-11150.063;  ML change (error):     0.010;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================                                                       ]
Iteration:75
ML:-11150.072;  ML change (error):     0.009;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================                                                      ]
Iteration:76
ML:-11150.080;  ML change (error):     0.008;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================                                                      ]
Iteration:77
ML:-11150.087;  ML change (error):     0.008;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================                                                      ]
Iteration:78
ML:-11150.094;  ML change (error):     0.007;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================                                                      ]
Iteration:79
ML:-11150.101;  ML change (error):     0.006;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================                                                      ]
Iteration:80
ML:-11150.107;  ML change (error):     0.006;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===================                                                     ]
Iteration:81
ML:-11150.112;  ML change (error):     0.006;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===================                                                     ]
Iteration:82
ML:-11150.117;  ML change (error):     0.005;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===================                                                     ]
Iteration:83
ML:-11150.122;  ML change (error):     0.005;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===================                                                     ]
Iteration:84
ML:-11150.126;  ML change (error):     0.004;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====================                                                    ]
Iteration:85
ML:-11150.130;  ML change (error):     0.004;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====================                                                    ]
Iteration:86
ML:-11150.134;  ML change (error):     0.004;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====================                                                    ]
Iteration:87
ML:-11150.138;  ML change (error):     0.003;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[====================                                                    ]
Iteration:88
ML:-11150.141;  ML change (error):     0.003;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====================                                                   ]
Iteration:89
ML:-11150.144;  ML change (error):     0.003;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====================                                                   ]
Iteration:90
ML:-11150.146;  ML change (error):     0.003;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====================                                                   ]
Iteration:91
ML:-11150.149;  ML change (error):     0.002;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=====================                                                   ]
Iteration:92
ML:-11150.151;  ML change (error):     0.002;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======================                                                  ]
Iteration:93
ML:-11150.153;  ML change (error):     0.002;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======================                                                  ]
Iteration:94
ML:-11150.155;  ML change (error):     0.002;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======================                                                  ]
Iteration:95
ML:-11150.157;  ML change (error):     0.002;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[======================                                                  ]
Iteration:96
ML:-11150.158;  ML change (error):     0.002;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======================                                                 ]
Iteration:97
ML:-11150.160;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======================                                                 ]
Iteration:98
ML:-11150.161;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======================                                                 ]
Iteration:99
ML:-11150.162;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=======================                                                 ]
Iteration:100
ML:-11150.164;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========================                                                ]
Iteration:101
ML:-11150.165;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========================                                                ]
Iteration:102
ML:-11150.166;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========================                                                ]
Iteration:103
ML:-11150.167;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========================                                                ]
Iteration:104
ML:-11150.167;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[========================                                                ]
Iteration:105
ML:-11150.168;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========================                                               ]
Iteration:106
ML:-11150.169;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========================                                               ]
Iteration:107
ML:-11150.170;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========================                                               ]
Iteration:108
ML:-11150.170;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=========================                                               ]
Iteration:109
ML:-11150.171;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========================                                              ]
Iteration:110
ML:-11150.171;  ML change (error):     0.001;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========================                                              ]
Iteration:111
ML:-11150.172;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========================                                              ]
Iteration:112
ML:-11150.172;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==========================                                              ]
Iteration:113
ML:-11150.173;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========================                                             ]
Iteration:114
ML:-11150.173;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========================                                             ]
Iteration:115
ML:-11150.173;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========================                                             ]
Iteration:116
ML:-11150.174;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===========================                                             ]
Iteration:117
ML:-11150.174;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============================                                            ]
Iteration:118
ML:-11150.174;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============================                                            ]
Iteration:119
ML:-11150.174;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============================                                            ]
Iteration:120
ML:-11150.175;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[============================                                            ]
Iteration:121
ML:-11150.175;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============================                                           ]
Iteration:122
ML:-11150.175;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============================                                           ]
Iteration:123
ML:-11150.175;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============================                                           ]
Iteration:124
ML:-11150.175;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=============================                                           ]
Iteration:125
ML:-11150.175;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============================                                          ]
Iteration:126
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============================                                          ]
Iteration:127
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============================                                          ]
Iteration:128
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============================                                          ]
Iteration:129
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==============================                                          ]
Iteration:130
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============================                                         ]
Iteration:131
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============================                                         ]
Iteration:132
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============================                                         ]
Iteration:133
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===============================                                         ]
Iteration:134
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================================                                        ]
Iteration:135
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================================                                        ]
Iteration:136
ML:-11150.176;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================================                                        ]
Iteration:137
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[================================                                        ]
Iteration:138
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================================                                       ]
Iteration:139
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================================                                       ]
Iteration:140
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================================                                       ]
Iteration:141
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[=================================                                       ]
Iteration:142
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================================                                      ]
Iteration:143
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================================                                      ]
Iteration:144
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================================                                      ]
Iteration:145
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[==================================                                      ]
Iteration:146
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===================================                                     ]
Iteration:147
ML:-11150.177;  ML change (error):     0.000;   Sigma^2:     0.001;     Sigma^2 change:     0.000
[===================================                                     ]
Iteration:148
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[================================================================        ]
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[================================================================        ]
========================================================================
Registration Performance Metrics
========================================================================
Time to initialize EM: 0.0028879642486572266
Time to initialize registration: 0.16175317764282227
Average Expectation Time:                    0.0345 +/- 0.0031
Average Maximization Time:                   0.0061 +/- 0.0007
Maximization Times - Per individual step
Average Update Transform Time:               0.0058 +/- 0.0007
Average Transform Time:                      0.0001 +/- 0.0000
Average Update Variance Time:                0.0001 +/- 0.0000

Number of iterations performed:          268
Error at time of finish:                 8.756614988669753e-09
time to get cdist: 0.18356680870056152

if I stop the process and continue then I'm getting the following error TypeError: Could not find a suitable VTK type for object while executing below line reg.view_meshes_colored_by_spectral_correspondences() complete error is as follows 

TypeError                                 Traceback (most recent call last)
<ipython-input-17-becf559b59fd> in <module>
----> 1 reg.view_meshes_colored_by_spectral_correspondences()

/usr/local/lib/python3.7/site-packages/pyfocusr-0.0.1-py3.7.egg/pyfocusr/focusr.py in view_meshes_colored_by_spectral_correspondences(self, x_translation, y_translation, z_translation, shadow)
    541 
    542         source_mesh = vtk_deep_copy(self.graph_source.vtk_mesh)
--> 543         source_mesh.GetPointData().SetScalars(numpy_to_vtk(self.corresponding_target_idx_for_each_source_pt))
    544 
    545         target_transform = vtk.vtkTransform()

/usr/local/lib/python3.7/site-packages/vtkmodules/util/numpy_support.py in numpy_to_vtk(num_array, deep, array_type)
    145         vtk_typecode = array_type
    146     else:
--> 147         vtk_typecode = get_vtk_array_type(z.dtype)
    148     result_array = create_vtk_array(vtk_typecode)
    149 

/usr/local/lib/python3.7/site-packages/vtkmodules/util/numpy_support.py in get_vtk_array_type(numpy_array_type)
     69             return vtk_type
     70     raise TypeError(
---> 71         'Could not find a suitable VTK type for %s' % (str(numpy_array_type)))
     72 
     73 def get_vtk_to_numpy_typemap():

TypeError: Could not find a suitable VTK type for object
gattia commented 4 years ago

Based on your outputs I am expecting that you are running the example notebook.

You said that you are stopping the process. Looks to me from your first print out that you are just missing three lines from the output of what I expect: 

time to linear sum assignment: 7.1949567794799805
Number of unique correspondences: 5000
Number of unique correspondences after smoothing: 4713

The values in there don't matter as much as the fact that those lines should be printed. This to me means that you arent finishing the linear_sum_assignment which is the hungarian algorithm described in the original paper (line 275 in pyfocusr.py). This is what is used to find correspondences between the meshes at the end of the registration. This makes sense why you are then able to run the next cell that plots the aligned spectral coordinates (because this part has completed - align the spectral coords), but then it fails when you try to run the other cells that include visualizations of the aligned meshes, which require correspondences to have been found and then new meshes to be generated from the correspondences.

Based on your print outs of how long things took, your registration is running faster than on my computer, and from my print out the linear_sum_assignment is only 7ish seconds. So, I would expect that it should occur pretty quickly. Did you let it run for some time? Without letting that part run/complete you won't get aligned meshes and there will be nothing to display in the second cell that is crashing, so those errors don't surprise me.

So... I guess my first suggestion is to just let it run for a while. If it is taking considerable time, I wonder whether there is some other bottleneck, your computations are faster than mine, maybe it is ram? How much ram do you have? Im running that step on a 2015 laptop with 16gb ram, so nothing crazy.

Lastly, have you changed any of the other default parameters in the example?

nuwanarti commented 4 years ago

I let it be for 2 hours but still it didn't complete the process

gattia commented 4 years ago

Please see my comment on the other issue (https://github.com/gattia/pyfocusr/issues/2). I updated some requirements and the build instructions on the main readme. This should mean that if you run the example notebook that everything should be identical to my setup. Hopefully this resolves any issues. If it still persists, if you could start by confirming what code you are running and how you are running it, what environment, your dependencies, and a script to reproduce the error that would help.

nuwanarti commented 4 years ago

Thankyou very much its working now on mac os catalina

gattia commented 4 years ago

Excellent.

Hope that it ends up serving your needs.