I am getting plenty of warning messages while running gitter.demo() command. Please see below.
Sathish

gitter.demo()
Processing sample.jpg ...
|======================================================================================| 100%

gitter v1.0.3 data file

Function call: gitter(image.file = f, verbose = "p")
Elapsed time: 5.63 secs
Plate format: 32 x 48 (1536)
Colony size statistics:
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0 196.8 303.0 262.7 356.0 670.0
Dat file (first 6 rows):
row col size circularity flags
1 1 1 357 0.5387 C
2 1 2 160 0.8029
3 1 3 393 0.8130
4 1 4 378 0.4710 C
5 1 5 261 0.1836 C
6 1 6 389 0.1588 S,C
Plate warnings:
high count of small colony sizes, high count of low colony circularity
There were 50 or more warnings (use warnings() to see the first 50)

warnings()
Warning messages:
1: In cor(ref, z, method = "spearman") : the standard deviation is zero
2: In cor(ref, z, method = "spearman") : the standard deviation is zero
3: In cor(ref, z, method = "spearman") : the standard deviation is zero
4: In cor(ref, z, method = "spearman") : the standard deviation is zero
5: In cor(ref, z, method = "spearman") : the standard deviation is zero
6: In cor(ref, z, method = "spearman") : the standard deviation is zero
7: In cor(ref, z, method = "spearman") : the standard deviation is zero
8: In cor(ref, z, method = "spearman") : the standard deviation is zero
9: In cor(ref, z, method = "spearman") : the standard deviation is zero
10: In cor(ref, z, method = "spearman") : the standard deviation is zero
11: In cor(ref, z, method = "spearman") : the standard deviation is zero
12: In cor(ref, z, method = "spearman") : the standard deviation is zero
13: In cor(ref, z, method = "spearman") : the standard deviation is zero
14: In cor(ref, z, method = "spearman") : the standard deviation is zero
15: In cor(ref, z, method = "spearman") : the standard deviation is zero
16: In cor(ref, z, method = "spearman") : the standard deviation is zero
17: In cor(ref, z, method = "spearman") : the standard deviation is zero
18: In cor(ref, z, method = "spearman") : the standard deviation is zero
19: In cor(ref, z, method = "spearman") : the standard deviation is zero
20: In cor(ref, z, method = "spearman") : the standard deviation is zero
21: In cor(ref, z, method = "spearman") : the standard deviation is zero
22: In cor(ref, z, method = "spearman") : the standard deviation is zero
23: In cor(ref, z, method = "spearman") : the standard deviation is zero
24: In cor(ref, z, method = "spearman") : the standard deviation is zero
25: In cor(ref, z, method = "spearman") : the standard deviation is zero
26: In cor(ref, z, method = "spearman") : the standard deviation is zero
27: In cor(ref, z, method = "spearman") : the standard deviation is zero
28: In cor(ref, z, method = "spearman") : the standard deviation is zero
29: In cor(ref, z, method = "spearman") : the standard deviation is zero
30: In cor(ref, z, method = "spearman") : the standard deviation is zero
31: In cor(ref, z, method = "spearman") : the standard deviation is zero
32: In cor(ref, z, method = "spearman") : the standard deviation is zero
33: In cor(ref, z, method = "spearman") : the standard deviation is zero
34: In cor(ref, z, method = "spearman") : the standard deviation is zero
35: In cor(ref, z, method = "spearman") : the standard deviation is zero
36: In cor(ref, z, method = "spearman") : the standard deviation is zero
37: In cor(ref, z, method = "spearman") : the standard deviation is zero
38: In cor(ref, z, method = "spearman") : the standard deviation is zero
39: In cor(ref, z, method = "spearman") : the standard deviation is zero
40: In cor(ref, z, method = "spearman") : the standard deviation is zero
41: In cor(ref, z, method = "spearman") : the standard deviation is zero
42: In cor(ref, z, method = "spearman") : the standard deviation is zero
43: In cor(ref, z, method = "spearman") : the standard deviation is zero
44: In cor(ref, z, method = "spearman") : the standard deviation is zero
45: In cor(ref, z, method = "spearman") : the standard deviation is zero
46: In cor(ref, z, method = "spearman") : the standard deviation is zero
47: In cor(ref, z, method = "spearman") : the standard deviation is zero
48: In cor(ref, z, method = "spearman") : the standard deviation is zero
49: In cor(ref, z, method = "spearman") : the standard deviation is zero
50: In cor(ref, z, method = "spearman") : the standard deviation is zero

sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gitter_1.0.4
loaded via a namespace (and not attached):
[1] abind_1.4-0 BiocGenerics_0.12.1 colorspace_1.2-4 digest_0.6.8
[5] EBImage_4.8.3 ggplot2_1.0.0 grid_3.1.2 gtable_0.1.2
[9] jpeg_0.1-8 labeling_0.3 lattice_0.20-29 locfit_1.5-9.1
[13] logging_0.7-103 MASS_7.3-35 munsell_0.4.2 parallel_3.1.2
[17] PET_0.4.9 plyr_1.8.1 png_0.1-7 proto_0.3-10
[21] Rcpp_0.11.3 reshape2_1.4.1 scales_0.2.4 stringr_0.6.2
[25] tiff_0.1-5 tools_3.1.2

Auto resize any image less than 1000 pixels in width to 1500. This avoids an error generated if a small size image is used.

Hi Omar,
Thanks for answering my previous issue.

I am getting the following error when I run gitter function.

gitter(image.file = "example_plate.tif", plate.format = c(32, 48), autorotate = F)

2015-03-25 19:19:00:INFO::Reading image from: example_plate.tif
Error in array(NA, dim = d[c(2, 1, 3)]) : 
negative length vectors are not allowed
In addition: Warning message:
In readTIFF(x, all = all, ...) :
TIFFReadDirectory: Unknown field with tag 59932 (0xea1c) encountered

After some inspection, I found that the error comes from tiff::readTIFF function. I do not understand the error per se. Is there a way to solve this issue? please let me know.

 a1 <- tiff::readTIFF("example_plate.tif")
 Warning message:
 In tiff::readTIFF("example_plate.tif") :  
 TIFFReadDirectory: Unknown field with tag 59932 (0xea1c) encountered

The "example_plate.tif" file is greater than 10MB which prevents me to attach it here. Please let me know if I need to send it through email.

Thank you
Sathish

Hi Omar

First of all, thanks for developing and maintaining the very useful R tool “gitter”.
I am using it to analyze our microbial plate images.
I just noticed that the Grayscales generated from gitter are a bit different than others.

After I checked the source code of gitter, I found there might be a problem in luminosity grey scale from GIMP.
Here are some problematic lines in your main.R
.readImage <- function(file){ n = basename(file) if(grepl('*.jpg$|*.jpeg$', file, ignore.case=T)){ return( readJPEG(file) ) }else if(grepl('*.tiff$', file, ignore.case=T)){ return( readTIFF(file) ) }else{ im = imageData( readImage(file) ) d = dim(im) M = array(NA, dim=d[c(2,1,3)]) M[,,1] = t(im[,,1]) if(d[3] > 1){ M[,,2] = t(im[,,2]) M[,,3] = t(im[,,3]) } return(M) } }

When it reads a JPEG or TIFF file by calling the function ” readJPEG”, the RGB order should be: 1:Red, 2: Green, 3:Blue

# Extract greyscale if(is.color){ if(prog) setTxtProgressBar(pb, 9) loginfo('\tDetected color image, extracting greyscale') # Luminosity grey scale from GIMP im.grey = (im[,,1]*0.72) + (im[,,2]*0.21) + (im[,,3]*0.07) #im.grey = im[,,1] }else{ loginfo('\tDetected greyscale image') im.grey = im # no color information }

Based on the Luminosity rule: https://en.wikipedia.org/wiki/Relative_luminance
Luminosity = 0.21 × Red + 0.72 × Green + 0.07 × Blue
so I suspected that the code here should be:
im.grey = (im[,,1]*0.21) + (im[,,2]*0.72) + (im[,,3]*0.07)

Is this correct??