Tip: Generating CSV for multi-channel histograms

[harukizaemon]

I wanted to generate a histogram as a CSV file for single and multi-channel images. The format I needed was each row represents an intensity, each column represents a channel. This differs from the standard VIPS histogram which is a single row with a column for each intensity value for a single channel only.

My initial approach was to take the histogram and iterate over each element of the histogram which worked great on RGBA (about 4.5 seconds) but for a 2-byte greyscale image, this took about 5 minutes.

The following runs in about 0.07 seconds for RGBA and about 5 seconds for the ushort:

image
  .hist_find
  .rot90
  .bandunfold
  .csvsave("histogram.csv", separator: ",")

There may well be a better way, but that worked for me :)

Oh, the only other thing I wish I could do is add column headers but I can live without them.

[jcupitt]

Nice writeup! I've made a tip label. Yup, bandunfold is supposed to make this kind of thing easy.

[Nakilon]

I have a problem using this bandunfold operation in shell.

vips crop $filepath_file temp.v $v_left $v_top $v_width $v_height && vips csvsave temp.v temp.csv && cat temp.csv

104	103	103	103
104	103	103	103
104	103	103	103
104	104	103	103
105	105	104	104

vips crop $filepath_file temp.v $v_left $v_top $v_width $v_height && vips bandunfold temp.v temp.v --factor 3 && vips csvsave temp.v temp.csv && cat temp.csv

0	0	0	0	0	0	0	0	0	0	0	0
0	0	0	0	0	0	0	0	0	0	0	0
0	0	0	0	0	0	0	0	0	0	0	0
0	0	0	0	0	0	0	0	0	0	0	0
0	0	0	0	0	0	0	0	0	0	0	0

It gives me all zeros.

$ file $filepath_file 
.../house.png: PNG image data, 120 x 162, 8-bit/color RGB, non-interlaced

[Nakilon]

I'm using vips-8.6.4 in this image: https://hub.docker.com/r/felixbuenemann/vips-alpine

[Nakilon]

Oh I made vips bandunfold temp.v temp_.v --factor 3 && vips csvsave temp_.v temp.csv and now it works. Seems like the bandunfold operation does not support the same filename as in and out.

[jcupitt]

Hello @Nakilon, yes, bandunfold streams the image, so you have to read and write to different files.

[Nakilon]

Lol I just realised I was confused by the ugly Github interface and all my comments went as top level replies but were intended to reply to your subthread. Probably not the first time I did that.

[kleisauke]

This discussion was originally inherited from issue #108, GitHub automatically transfers the responses as top-level.

[Nakilon]

Oh I see. Thank you for clarification.