‎Python

← Older revision Revision as of 23:34, 18 July 2018 (6 intermediate revisions by the same user not shown)Line 46: Line 46:  ==<font color='ForestGreen'>TIFF stacks for ML</font>== ==<font color='ForestGreen'>TIFF stacks for ML</font>==  [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] −[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.2 Decoded 'value'-layers]]+[[File:Tiff layers.jpeg|thumb|400px|Fig.2 TIFF imagestack layers]] −[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]]+[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.3 Decoded 'value'-layers]] −* What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]:+[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.4 Data layers]]  +* The TIFF stack format is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]:  +** 8 bpp  +** layer dimensions 2916x2178  ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other''']  *** '''diagm-pair''' *** '''diagm-pair''' Line 55: Line 58:  *** '''vert-pairs''' *** '''vert-pairs'''  *** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity *** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity −* Essentially it’s a normal TIFF image stack with several headers modified:+** The layers are tiled - tiles' wxh is read from the header - currently it's 9x9, making it 324x242 tiles total. −** ImageDescription (tag[270]) contains a string with info about number of images, slices+** The values in the '''other''' layer are encoded per tile. −** tag[50838] – a list of layers names’ lengths+** Essentially it’s a normal TIFF image stack with several headers modified: −** tag[50839] – binary string with encoded layers labels and extra info+*** ImageDescription (tag[270]) contains a string with info about number of images, slices  +*** tag[50838] – a list of layers names’ lengths  +*** tag[50839] – binary string with encoded layers labels and extra info  * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack  * There are a few ways to view the stack: * There are a few ways to view the stack: Line 110: Line 115:     Upon opening tiff the image will be a numpy array of shape '''(height,width,layer)''' - for further processing it is reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example: Upon opening tiff the image will be a numpy array of shape '''(height,width,layer)''' - for further processing it is reshaped to '''(height_in_tiles, width_in_tiles, tile_height, tile_width, layer)''', example: −  <font size='2'>tiff stack shape: (2178, 2916, 5)+  <font size='2'>original tiff stack shape: (2178, 2916, 5)    image data:  (242, 324, 9, 9, 4)   image data:  (242, 324, 9, 9, 4)    values data: (242, 324, 3)</font>   values data: (242, 324, 3)</font> Oleg

Oleg K Dzhimiev committed changes to the Elphel git project :
Update README.md

‎TIFF stacks for ML

← Older revision Revision as of 23:20, 18 July 2018 (4 intermediate revisions by the same user not shown)Line 46: Line 46:  ==<font color='ForestGreen'>TIFF stacks for ML</font>== ==<font color='ForestGreen'>TIFF stacks for ML</font>==  [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] −[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.2 Decoded 'value'-layers]]+[[File:Tiff layers.jpeg|thumb|400px|Fig.2 TIFF imagestack layers]] −[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]]+[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.3 Decoded 'value'-layers]] −* What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]:+[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.4 Data layers]]  +* The TIFF stack format is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]:  +** 8 bpp  +** layer dimensions 2916x2178  ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other''']  *** '''diagm-pair''' *** '''diagm-pair''' Line 55: Line 58:  *** '''vert-pairs''' *** '''vert-pairs'''  *** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity *** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity −* Essentially it’s a normal TIFF image stack with several headers modified:+** The layers are tiled - tiles' wxh is read from the header - currently it's 9x9, making it 324x242 tiles total. −** ImageDescription (tag[270]) contains a string with info about number of images, slices+** The values in the '''other''' layer are encoded per tile. −** tag[50838] – a list of layers names’ lengths+** Essentially it’s a normal TIFF image stack with several headers modified: −** tag[50839] – binary string with encoded layers labels and extra info+*** ImageDescription (tag[270]) contains a string with info about number of images, slices  +*** tag[50838] – a list of layers names’ lengths  +*** tag[50839] – binary string with encoded layers labels and extra info  * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack  * There are a few ways to view the stack: * There are a few ways to view the stack: Line 70: Line 75:  * <font color='DarkGreen'>'''Convert layers to numpy arrays (split into tiles or optionally not split) for further computations and plotting'''</font> * <font color='DarkGreen'>'''Convert layers to numpy arrays (split into tiles or optionally not split) for further computations and plotting'''</font>  Example (more examples are commented out in the __main__ section of the script): Example (more examples are commented out in the __main__ section of the script): −  <font size='1' style='line-height:0.5;'>'''~$ python3 imagej_tiff.py 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff'''+  <font size='1' style='line-height:0.5;'># Dependencies:  + # - Python 3.5.2 (not strict)  + # - Pillow 5.1.0+ (strict)  + # - Numpy 1.14.2 (not strict)  + # - Matplotlib 2.2.2 (not strict)  +  + '''~$ python3 imagej_tiff.py 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff'''    time: 1531344391.7055812   time: 1531344391.7055812    time: 1531344392.5336654   time: 1531344392.5336654 Oleg

← Older revision Revision as of 21:41, 18 July 2018 Line 46: Line 46:  ==<font color='ForestGreen'>TIFF stacks for ML</font>== ==<font color='ForestGreen'>TIFF stacks for ML</font>==  [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] −[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.2 Decoded 'value'-layers]]+[[File:Tiff layers.jpeg|thumb|400px|Fig.2 TIFF imagestack layers]] −[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]]+[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.3 Decoded 'value'-layers]]  +[[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.4 Data layers]]  * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]:  ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] ** 5 layers in the stack: ['''diagm-pair''', '''diago-pair''', '''hor-pairs''', '''vert-pairs''', '''other'''] Oleg

Oleg uploaded File:Tiff layers.jpeg

New page

== Licensing ==
{{CC }} Oleg

‎TIFF stacks for ML

← Older revision Revision as of 21:40, 18 July 2018 (One intermediate revision by the same user not shown)Line 46: Line 46:  ==<font color='ForestGreen'>TIFF stacks for ML</font>== ==<font color='ForestGreen'>TIFF stacks for ML</font>==  [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ, one of the layers]] −[[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]]+[[File:Ml tiff stack python values.jpeg|thumb|400px|Fig.2 Decoded 'value'-layers]]  [[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]] [[File:Ml tiff stack python data layers.jpeg|thumb|500px|Fig.3 Data layers]]  * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: * What's in each stack is described in the [https://community.elphel.com/files/presentations/Elphel_TP-CNN_slides.pdf presentation for CVPR2018, pp.19-21]: Line 55: Line 55:  *** '''vert-pairs''' *** '''vert-pairs'''  *** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity *** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity  +* Essentially it’s a normal TIFF image stack with several headers modified:  +** ImageDescription (tag[270]) contains a string with info about number of images, slices  +** tag[50838] – a list of layers names’ lengths  +** tag[50839] – binary string with encoded layers labels and extra info  * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack * The source files are processed using a plugin for ImageJ, the output file for each set is a tiff stack  * There are a few ways to view the stack: * There are a few ways to view the stack:  ====ImageJ==== ====ImageJ==== −ImageJ - it has a native support for stacks, each stack has a name label stored (along with related xml info) in the ImageJ tiff tags. To read tiff tags in ImageJ, go '''Image > Show Info...'''+ImageJ (or Fiji) - it has a native support for stacks, each stack has a name label stored (along with related xml info) in the ImageJ tiff tags. To read tiff tags in ImageJ, go '''Image > Show Info...'''  ====Python==== ====Python====  '''1.''' Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''1.''' Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: Oleg

Oleg uploaded a new version of File:Ml tiff stack python values.jpeg

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== Licensing ==
{{CC }} Oleg

Andrey Filippov committed changes to the Elphel git project :
handling error (probably cons. of fronto)

Oleg Dzhimiev committed changes to the Elphel git project :
token loading

Oleg Dzhimiev committed changes to the Elphel git project :
fix map init

Oleg Dzhimiev committed changes to the Elphel git project :
fix map init

Oleg Dzhimiev committed changes to the Elphel git project :
fix map init

Oleg Dzhimiev committed changes to the Elphel git project :
added mapbox layers

Oleg Dzhimiev committed changes to the Elphel git project :
map autofit

Oleg Dzhimiev committed changes to the Elphel git project :
added groups for linking

Oleg Dzhimiev committed changes to the Elphel git project :
fixed hardcoded paths

Oleg Dzhimiev committed changes to the Elphel git project :
1. pass zooom and lat;lng from index to viewer and back 2. center on dblclick, no center on click 3. minor error fix

Andrey Filippov committed changes to the Elphel git project :
debug output

Andrey Filippov committed changes to the Elphel git project :
disable some debug print that caused errors in multithreaded mode

AndreyFilippov committed changes to the Elphel git project :
detecting periodic features (unfinished)