Re: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe
It depends on what is wrong with the data (I haven't checked it). Morpheus et al. can be used to correct data after visual inspection or mark bad data points as missing or delete whole sets of coordinates for particular points. The easiest way to do this is to get the data into a form importable by Morpheus - NTSYSpc is the easiest, and import the data. You can then set up links between points (there is a menu option). Then, you can just page through the objects looking for one whose links are obviously wrong. You can then swap points (another menu option) until they are in the correct order. For this, it is useful to use the plot Opts button to set the point plotting symbol as "number", which locates the points with their number, e.g., "1", "2", etc. You can also mark any offending points (with genuinely bad data) as "missing" or delete points/landmarks. If there are too few or too many, you can insert missing points (which will be marked as missing data) or delete specific points from specific objects. Another suggestion to find objects with bad points is to do a PCA plot (I use R) to check for any outliers. If there are a few scattered points with missing data at the end of all of this, the data can be filled in using missing data imputation - mean substitution is the only method currently implemented. Mean substitution generally does not affect parameter estimates, but does result in error estimates that are undervalued - there is more variance than apparent in the data since mean values were substituted for missing data. -ds PS: NTSYSpc format for import. On the first line, 1 is NTSYS for rectangular data matrix, n is for the number of objects in the file (you have to provide a number, not 'n'); a number representing the number of landmarks, p, times the number of dimensions, 3 in your case; and a '0' indicating there are no missing data in the data set. If there are missing data, then the '0' is replace by something like "1 -999", where the '1' indicates the presence of missing data and the next item, e.g., -999, is the code used to indicate missing data... 1 n nDimxp 0 x1 y1 z1 x2 y2 z2 ... xp yp zp ...repeated (except for the first line) for more objects On 5/7/19 8:09 AM, Azadeh Mohaseb wrote: Dear all I am a post-doc researcher on GMM and I work on equids bones. Recently, I digitized some modern equid bones by a microscribe and then I realized that the 3d coordinates of some of these individuals are not correcte. As I don't have access to these bones to digitize them again, I wondered if you could help me to fix this problem. I send you the correct coordinates of one individual and the incorrect coordinates of another one. These two individuals have been digitized at the same time, with same microscribe and the same settings on machine and software. Individual 1: correct 228.6438203.1991156.5325 220.2511204.6701143.3459 223.9106202.3835121.6829 242.5923225.1355121.4050 240.4551225.8690136.0673 238.9128226.4731141.2689 240.9662226.0292146.4538 243.8571223.4773158.7283 248.3989203.3913162.7939 247.9284204.2474147.2226 249.7594202.0327140.3145 247.2640205.0845134.1143 246.3540204.5467115.9491 88.1469 334.5199162.2996 79.0490 330.4259152.7271 74.0790 325.4809142.4243 79.8139 324.6076119.4693 86.4637 331.0746115.0139 88.8453 333.9695120.4097 87.0741 333.9286128.0646 85.8100 336.1603144.5840 83.5972 335.3779150.5125 90.8324 337.0566156.8697 92.3339 337.9303154. 87.5753 339.9321145.9987 93.6211 346.3407145.2005 98.7993 344.1494152.6361 89.2627 341.3373127.1407 91.0691 339.7504123.6672 94.9706 342.5350123.9575 93.9787 344.1297127.5435 Individual 2: incorrect 117.190772.8549 331.5414 63.8556 106.7571324.6544 64.2134 108.2755327.6326 125.581822.1134 446.8474 117.373526.4359 458.0952 110.488427.9800 458.7083 111.163221.4185 461.2170 106.153618.8334 468.0809 71.8894 25.9454 248.6469 49.2014 61.3649 250.9960 50.9447 62.2230 251.7744 31.1992 99.5425 270.7333 38.6410 96.3750 268.3234 104.840276.1165 472.1013 104.034379.0076 464.1394 81.7345 108.8425464.0654 85.9537 128.9866461.4308 88.6260 142.0624468.9539 96.1857 130.2672474.6507 85.1190 135.9783473.3503 7
RE: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe
To add briefly to Dennis' comment. If landmark estimation is the route taken, both TPS-based and regression-based imputation are implemented in geomorph. Dean Dr. Dean C. Adams Director of Graduate Education, EEB Program Professor Department of Ecology, Evolution, and Organismal Biology Iowa State University https://www.eeob.iastate.edu/faculty/adams/ phone: 515-294-3834 -Original Message- From: morphmet Sent: Tuesday, May 7, 2019 8:18 AM To: morphmet@morphometrics.org Subject: Re: [MORPHMET] How to fix erroneous 3D coordinates took by microscribe It depends on what is wrong with the data (I haven't checked it). Morpheus et al. can be used to correct data after visual inspection or mark bad data points as missing or delete whole sets of coordinates for particular points. The easiest way to do this is to get the data into a form importable by Morpheus - NTSYSpc is the easiest, and import the data. You can then set up links between points (there is a menu option). Then, you can just page through the objects looking for one whose links are obviously wrong. You can then swap points (another menu option) until they are in the correct order. For this, it is useful to use the plot Opts button to set the point plotting symbol as "number", which locates the points with their number, e.g., "1", "2", etc. You can also mark any offending points (with genuinely bad data) as "missing" or delete points/landmarks. If there are too few or too many, you can insert missing points (which will be marked as missing data) or delete specific points from specific objects. Another suggestion to find objects with bad points is to do a PCA plot (I use R) to check for any outliers. If there are a few scattered points with missing data at the end of all of this, the data can be filled in using missing data imputation - mean substitution is the only method currently implemented. Mean substitution generally does not affect parameter estimates, but does result in error estimates that are undervalued - there is more variance than apparent in the data since mean values were substituted for missing data. -ds PS: NTSYSpc format for import. On the first line, 1 is NTSYS for rectangular data matrix, n is for the number of objects in the file (you have to provide a number, not 'n'); a number representing the number of landmarks, p, times the number of dimensions, 3 in your case; and a '0' indicating there are no missing data in the data set. If there are missing data, then the '0' is replace by something like "1 -999", where the '1' indicates the presence of missing data and the next item, e.g., -999, is the code used to indicate missing data... 1 n nDimxp 0 x1 y1 z1 x2 y2 z2 ... xp yp zp ...repeated (except for the first line) for more objects On 5/7/19 8:09 AM, Azadeh Mohaseb wrote: > Dear all > I am a post-doc researcher on GMM and I work on equids bones. Recently, I > digitized some modern equid bones by a microscribe and then I realized that > the 3d coordinates of some of these individuals are not correcte. > As I don't have access to these bones to digitize them again, I wondered if > you could help me to fix this problem. > I send you the correct coordinates of one individual and the incorrect > coordinates of another one. These two individuals have been digitized at the > same time, with same microscribe and the same settings on machine and > software. > > Individual 1: correct > > 228.6438 203.1991156.5325 > 220.2511 204.6701143.3459 > 223.9106 202.3835121.6829 > 242.5923 225.1355121.4050 > 240.4551 225.8690136.0673 > 238.9128 226.4731141.2689 > 240.9662 226.0292146.4538 > 243.8571 223.4773158.7283 > 248.3989 203.3913162.7939 > 247.9284 204.2474147.2226 > 249.7594 202.0327140.3145 > 247.2640 205.0845134.1143 > 246.3540 204.5467115.9491 > 88.1469 334.5199162.2996 > 79.0490 330.4259152.7271 > 74.0790 325.4809142.4243 > 79.8139 324.6076119.4693 > 86.4637 331.0746115.0139 > 88.8453 333.9695120.4097 > 87.0741 333.9286128.0646 > 85.8100 336.1603144.5840 > 83.5972 335.3779150.5125 > 90.8324 337.0566156.8697 > 92.3339 337.9303154. > 87.5753 339.9321145.9987 > 93.6211 346.3407145.2005 > 98.7993 344.1494152.6361 > 89.2627 341.3373127.1407 > 91.0691
