source: readme.txt

Last change on this file was 460:47510918e4ef, checked in by Dmitry Fedorov <fedorov@…>, 6 years ago

updated readme

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1BioImageConvertor ver: 2.0
2
3Author: Dima V. Fedorov <http://www.dimin.net/>
4
5Arguments: [[-i | -o] FILE_NAME | -t FORMAT_NAME ]
6
7Ex: imgcnv -i 1.jpg -o 2.tif -t TIFF
8
9-brightnesscontrast   - color brightness/contrast adjustment: brightness,contrast, each in range [-100,100], ex: -brightnesscontrast 50,-40
10
11
12-c                    - additional channels input file name, multiple -c are allowed, in which case multiple channels will be added, -c image must have the same size
13
14-create               - creates a new image with w-width, h-height, z-num z, t-num t, c - channels, d-bits per channel, ex: -create 100,100,1,1,3,8
15
16-deinterlace          - deinterlaces input image with one of the available methods, ex: -deinterlace avg
17    odd  - Uses odd lines
18    even - Uses even lines
19    avg  - Averages lines
20
21
22-depth                - output depth (in bits) per channel, allowed values now are: 8,16,32,64, ex: -depth 8,D,U
23  if followed by comma and [F|D|T|E] allowes to choose LUT method
24    F - Linear full range
25    D - Linear data range (default)
26    T - Linear data range with tolerance ignoring very low values
27    E - equalized
28    C - type cast
29    N - floating point number [0, 1]
30    G - Gamma correction, requires setting -gamma
31    L - Levels: Min, Max and Gamma correction, requires setting -gamma, -maxv and -minv
32  if followed by comma and [U|S|F] the type of output image can be defined
33    U - Unsigned integer (with depths: 8,16,32,64) (default)
34    S - Signed integer (with depths: 8,16,32,64)
35    F - Float (with depths: 32,64,80)
36  if followed by comma and [CS|CC] sets channel mode
37    CS - channels separate, each channel enhanced separately (default)
38    CC - channels combined, channels enhanced together preserving mutual relationships
39
40
41-display              - creates 3 channel image with preferred channel mapping
42
43-enhancemeta          - Enhances an image beased on preferred settings, currently only CT hounsfield mode is supported, ex: -enhancemeta
44
45-filter               - filters input image, ex: -filter edge
46    edge - first derivative
47    otsu - b/w masked image
48    wndchrmcolor - color quantized hue image
49
50-flip                 - flip the image vertically
51
52-fmt                  - print supported formats
53
54-fmthtml              - print supported formats in HTML
55
56-fmtxml               - print supported formats in XML
57
58-fuse                 - Changes order and number of channels in the output additionally allowing combining channels
59Channels separated by comma specifying output channel order (0 means empty channel)
60multiple channels can be added using + sign, ex: -fuse 1+4,2+4+5,3
61
62-fuse6                - Produces 3 channel image from up to 6 channels
63Channels separated by comma in the following order: Red,Green,Blue,Yellow,Magenta,Cyan,Gray
64(0 or empty value means empty channel), ex: -fuse6 1,2,3,4
65
66
67-fusegrey             - Produces 1 channel image averaging all input channels, uses RGB weights for 3 channel images and equal weights for all others, ex: -fusegrey
68
69-fusemeta             - Produces 3 channel image getting fusion weights from embedded metadata, ex: -fusemeta
70
71-fusemethod           - Defines fusion method, ex: -fusemethod a
72  should be followed by comma and [a|m]
73    a - Average
74    m - Maximum
75
76
77-fusergb              - Produces 3 channel image from N channels, for each channel an RGB weight should be given
78Component contribution are separated by comma and channels are separated by semicolon:
79(0 or empty value means no output), ex: -fusergb 100,0,0;0,100,100;0;0,0,100
80Here ch1 will go to red, ch2 to cyan, ch3 not rendered and ch4 to blue
81
82
83-gamma                - sets gamma for histogram conversion: 0.5, 1.0, 2.2, etc, ex: -gamma 2.2
84
85
86-geometry             - redefines geometry for any incoming image with: z-num z, t-num t and optionally c-num channels, ex: -geometry 5,1 or -geometry 5,1,3
87
88-hounsfield           - enhances CT image using hounsfield scale, ex: -hounsfield 8,U,40,80
89  output depth (in bits) per channel, allowed values now are: 8,16,32,64
90  followed by comma and [U|S|F] the type of output image can be defined
91    U - Unsigned integer (with depths: 8,16,32,64) (default)
92    S - Signed integer (with depths: 8,16,32,64)
93    F - Float (with depths: 32,64,80)
94  followed by comma and window center
95  followed by comma and window width
96  optionally followed by comma and slope
97  followed by comma and intercept, ex: -hounsfield 8,U,40,80,1.0,-1024.0
98  if slope and intercept are not set, their values would be red from DICOM metadata, defaulting to 1 and -1024
99
100
101-i                    - input file name, multiple -i are allowed, but in multiple case each will be interpreted as a 1 page image.
102
103-ihst                 - read image histogram from the file and use for nhancement operations
104
105-il                   - list input file name, containing input file name per line of the text file
106
107-info                 - print image info
108
109-levels               - color levels adjustment: min,max,gamma, ex: -levels 15,200,1.2
110
111
112-loadomexml           - reads OME-XML from a file and writes if output format is OME-TIFF
113
114-maxv                 - sets max value for histogram conversion, ex: -maxv 240
115
116
117-meta                 - print image's meta-data
118
119-meta-custom          - print image's custom meta-data fields
120
121-meta-parsed          - print image's parsed meta-data, excluding custom fields
122
123-meta-raw             - print image's raw meta-data in one huge pile
124
125-meta-tag             - prints contents of a requested tag, ex: -tag pixel_resolution
126
127-minv                 - sets min value for histogram conversion, ex: -minv 20
128
129
130-mirror               - mirror the image horizontally
131
132-mosaic               - compose an image from aligned tiles, ex: -mosaic 512,20,11
133  Arguments are defined as SZ,NX,NY where:
134    SZ: defines the size of the tile in pixels with width equal to height
135    NX - number of tile images in X direction    NY - number of tile images in Y direction
136
137-multi                - creates a multi-paged image if possible (TIFF,AVI), enabled by default
138
139-negative             - returns negative of input image
140
141-no-overlap           - Skips frames that overlap with the previous non-overlapping frame, ex: -no-overlap 5
142  argument defines maximum allowed overlap in %, in the example it is 5%
143
144
145-norm                 - normalize input into 8 bits output
146
147-o                    - output file name
148
149-ohst                 - write image histogram to the file
150
151-ohstxml              - write image histogram to the XML file
152
153-options              - specify encoder specific options, ex: -options "fps 15 bitrate 1000"
154
155Video files AVI, SWF, MPEG, etc. encoder options:
156  fps N - specify Frames per Second, where N is a float number, if empty or 0 uses default, ex: -options "fps 29.9"
157  bitrate N - specify bitrate in Mb, where N is an integer number, if empty or 0 uses default, ex: -options "bitrate 10000000"
158
159JPEG encoder options:
160  quality N - specify encoding quality 0-100, where 100 is best, ex: -options "quality 90"
161  progressive no - disables progressive JPEG encoding
162  progressive yes - enables progressive JPEG encoding (default)
163
164TIFF encoder options:
165  compression N - where N can be: none, packbits, lzw, fax, ex: -options "compression none"
166  tiles N - write tiled TIFF where N defined tile size, ex: tiles -options "512"
167  pyramid N - writes TIFF pyramid where N is a storage type: subdirs, topdirs, ex: -options "compression lzw tiles 512 pyramid subdirs"
168
169
170
171-overlap-sampling     - Defines sampling after overlap detected until no overlap, used to reduce sampling if overlapping, ex: -overlap-sampling 5
172
173
174-page                 - pages to extract, should be followed by page numbers separated by comma, ex: -page 1,2,5
175  page enumeration starts at 1 and ends at number_of_pages
176  page number can be a dash where dash will be substituted by a range of values, ex: -page 1,-,5  if dash is not followed by any number, maximum will be used, ex: '-page 1,-' means '-page 1,-,number_of_pages'
177  if dash is a first caracter, 1 will be used, ex: '-page -,5' means '-page 1,-,5'
178
179-pixelcounts          - counts pixels above and below a given threshold, requires output file name to store resultant XML file, ex: -pixelcounts 120
180
181
182-project              - combines by MAX all inout frames into one
183
184-projectmax           - combines by MAX all inout frames into one
185
186-projectmin           - combines by MIN all inout frames into one
187
188-raw                  - reads RAW image with w,h,c,d,p,e,t,interleaved ex: -raw 100,100,3,8,10,0,uint8,1
189  w-width, h-height, c - channels, d-bits per channel, p-pages
190  e-endianness(0-little,1-big), if in doubt choose 0
191  t-pixel type: int8|uint8|int16|uint16|int32|uint32|float|double, if in doubt choose uint8
192  interleaved - (0-planar or RRRGGGBBB, 1-interleaved or RGBRGBRGB)
193
194-rawmeta              - print image's raw meta-data in one huge pile
195
196-rearrange3d          - Re-arranges dimensions of a 3D image, ex: -rearrange3d xzy
197  should be followed by comma and [xzy|yzx]
198    xzy - rearranges XYZ -> XZY
199    yzx - rearranges XYZ -> YZX
200
201
202-reg-points           - Defines quality for image alignment in number of starting points, ex: -reg-points 200
203  Suggested range is in between 32 and 512, more points slow down the processing
204
205
206-remap                - Changes order and number of channels in the output, channel numbers are separated by comma (0 means empty channel), ex: -remap 1,2,3
207
208-res-level            - extract a specified pyramidal level, ex: -res-level 4
209    L - is a resolution level, L=0 is native resolution, L=1 is 2X smaller, L=2 is 4X smaller, and so on
210
211-resample             - Is the same as resize, the difference is resample is brute force and resize uses image pyramid for speed
212
213-resize               - should be followed by: width and height of the new image, ex: -resize 640,480
214  if one of the numbers is ommited or 0, it will be computed preserving aspect ratio, ex: -resize 640,,NN
215  if followed by comma and [NN|BL|BC] allowes to choose interpolation method, ex: -resize 640,480,NN
216    NN - Nearest neighbor (default)
217    BL - Bilinear
218    BC - Bicubic
219  if followed by comma [AR|MX|NOUP], the sizes will be limited:
220    AR - resize preserving aspect ratio, ex: 640,640,NN,AR
221    MX|NOUP - size will be used as maximum bounding box, preserving aspect ratio and not upsampling, ex: 640,640,NN,MX
222
223-resize3d             - performs 3D interpolation on an input image, ex: -resize3d 640,480,16
224  if one of the W/H numbers is ommited or 0, it will be computed preserving aspect ratio, ex: -resize3d 640,,16,NN
225  if followed by comma and [NN|BL|BC] allowes to choose interpolation method, ex: -resize3d 640,480,16,BC
226    NN - Nearest neighbor (default)
227    TL - Trilinear
228    TC - Tricubic
229  if followed by comma AR, the size will be used as maximum bounding box to resize preserving aspect ratio, ex: 640,640,16,BC,AR
230
231-resolution           - redefines resolution for any incoming image with: x,y,z,t where x,y,z are in microns and t in seconds  ex: -resolution 0.012,0.012,1,0
232
233-roi                  - regions of interest, should be followed by: x1,y1,x2,y2 that defines ROI rectangle, ex: -roi 10,10,100,100
234  if x1 or y1 are ommited they will be set to 0, ex: -roi ,,100,100 means 0,0,100,100
235  if x2 or y2 are ommited they will be set to image size, ex: -roi 10,10,, means 10,10,width-1,height-1
236  if more than one region of interest is desired, specify separated by ';', ex: -roi 10,10,100,100;20,20,120,120
237  in case of multiple regions, specify a template for output file creation with following variables, ex: -template {output_filename}_{x1}.{y1}.{x2}.{y2}.tif
238
239-rotate               - rotates the image by deg degrees, only accepted valueas now are: 90, -90, 180, guess
240guess will extract suggested rotation from EXIF
241
242-sampleframes         - samples for reading every Nth frame (useful for videos), ex: -sampleframes 5
243
244-single               - disables multi-page creation mode
245
246-skip-frames-leading  - skip N initial frames of a sequence, ex: -skip-frames-leading 5
247
248-skip-frames-trailing - skip N final frames of a sequence, ex: -skip-frames-trailing 5
249
250-stretch              - stretch data to it's full range
251
252-superpixels          - Segments image using SLIC superpixel method, takes region size and regularization, ex: -superpixels 16,0.2
253    region size is in pixels
254    regularization - [0-1], where 0 means shape is least regular
255
256-supported            - prints yes/no if the file can be decoded
257
258-t                    - output format
259
260-template             - Define a template for file names, ex: -template {output_filename}_{n}.tif
261  templates specify variables inside {} blocks, available variables vary for different processing
262
263-textureatlas         - Produces a texture atlas 2D image for 3D input images
264
265-texturegrid          - Creates custom texture atlas with: rows,cols ex: -texturegrid 5,7
266
267
268-threshold            - thresholds the image, ex: -threshold 120,upper
269  value is followed by comma and [lower|upper|both] to selet thresholding method
270    lower - sets pixels below the threshold to lowest possible value
271    upper - sets pixels above or equal to the threshold to highest possible value
272    both - sets pixels below the threshold to lowest possible value and above or equal to highest
273
274
275-tile                 - tile the image and store tiles in the output directory, ex: -tile 256
276  argument defines the size of the tiles in pixels
277  tiles will be created based on the outrput file name with inserted L, X, Y, where    L - is a resolution level, L=0 is native resolution, L=1 is 2x smaller, and so on    X and Y - are tile indices in X and Y, where the first tile is 0,0, second in X is: 1,0 and so on  ex: '-o my_file.jpg' will produce files: 'my_file_LLL_XXX_YYY.jpg'
278
279  Providing more arguments will instruct extraction of embedded tiles with -tile SZ,XID,YID,L ex: -tile 256,2,4,3
280    SZ: defines the size of the tile in pixels
281    XID and YID - are tile indices in X and Y, where the first tile is 0,0, second in X is: 1,0 and so on    L - is a resolution level, L=0 is native resolution, L=1 is 2x smaller, and so on
282
283-transform            - transforms input image, ex: -transform fft
284    chebyshev - outputs a transformed image in double precision
285    fft - outputs a transformed image in double precision
286    radon - outputs a transformed image in double precision
287    wavelet - outputs a transformed image in double precision
288
289-transform_color      - transforms input image 3 channel image in color space, ex: -transform_color rgb2hsv
290    hsv2rgb - converts HSV -> RGB
291    rgb2hsv - converts RGB -> HSV
292
293-v                    - prints version
294
295-verbose              - output information about the processing progress, ex: -verbose
296  verbose allows argument that defines the amount of info, currently: 1 and 2
297  where: 1 is the light info output, 2 is full output
298
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