Mercurial > repos > goeckslab > rename_tiff_channels

comparison rename_tiff_channels.xml @ 5:61fd94c7ce42 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit bc438db690e41823909b32b693f297d942433a43
author goeckslab
date Thu, 11 Jul 2024 22:41:10 +0000
parents d2c59a1ac0c4
children 4763362914f4
comparison
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4:55bc102d7709 5:61fd94c7ce42
31 <configfiles> 31 <configfiles>
32 <configfile name = "script"> 32 <configfile name = "script">
33 import os 33 import os
34 import sys 34 import sys
35 import argparse 35 import argparse
36 from itertools import cycle
36 import pandas as pd 37 import pandas as pd
37 import ome_types 38 import ome_types
38 from ome_types.model import channel 39 from ome_types.model import channel, Color
39 from tifffile import tiffcomment 40 from tifffile import tiffcomment
41
42 # setting default colors to match avivator
43 colors = [
44 (0,0,255,1.0), # blue
45 (0,255,0,1.0), # green
46 (255,0,255,1.0), # magenta
47 (255,255,0,1.0), # yellow
48 (255,127,0,1.0), # orange
49 (0,255,255,1.0), # cyan
50 (255,255,255,1.0), # white
51 (255,0,0,1.0) # red
52 ]
53
54 # convert to repeatable object of primitive int colors
55 color_cycle = cycle([Color(c).as_int32() for c in colors])
40 56
41 cwd = os.getcwd() 57 cwd = os.getcwd()
42 58
43 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv')) 59 channels_df = pd.read_csv(os.path.join(cwd, 'channels.csv'))
44 60
49 65
50 for c_idx, channel in enumerate(level.pixels.channels): 66 for c_idx, channel in enumerate(level.pixels.channels):
51 67
52 new_name = channels_df.loc[c_idx, 'marker_name'] 68 new_name = channels_df.loc[c_idx, 'marker_name']
53 channel.name = new_name 69 channel.name = new_name
70 channel.color = next(color_cycle)
54 71
55 if l_idx == 0: 72 if l_idx == 0:
56 73
57 print(f"Channel {c_idx} renamed to {new_name}") 74 print(f"Channel {c_idx} renamed to {new_name}")
58 75
70 <outputs> 87 <outputs>
71 <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/> 88 <data name="renamed_image" format="ome.tiff" from_work_dir="renamed_image.ome.tiff" label="${tool.name} on ${on_string}"/>
72 </outputs> 89 </outputs>
73 <tests> 90 <tests>
74 <test> 91 <test>
75 <param name="image" value="rename_test.tiff" /> 92 <param name="image" value="rename_test.ome.tiff" />
76 <param name="channel_csv" value="rename_channels.csv" /> 93 <param name="channel_csv" value="rename_channels.csv" />
77 <output name="renamed_image" ftype="ome.tiff"> 94 <output name="renamed_image" ftype="ome.tiff">
78 <assert_contents> 95 <assert_contents>
79 <has_size value="44000" delta="1000" /> 96 <has_size value="899000" delta="50000" />
80 </assert_contents> 97 </assert_contents>
81 </output> 98 </output>
82 <assert_stdout> 99 <assert_stdout>
83 <has_text text="Channel 0 renamed to DNA_6" /> 100 <has_text text="Channel 0 renamed to DNA_6" />
84 <has_text text="Updated OME-TIFF metadata" /> 101 <has_text text="Updated OME-TIFF metadata" />