‎Usage

← Older revision Revision as of 06:31, 24 July 2018 Line 18: Line 18:  Copyright &copy; {{CURRENTYEAR}} Elphel Inc. Copyright &copy; {{CURRENTYEAR}} Elphel Inc.    −Licensed under [https://ohwr.org/cernohl CERN OHL v.1.1], [https://www.gnu.org/copyleft/fdl.html GNU FDL v.1.3]+Licensed under [https://www.ohwr.org/licenses/cern-ohl/license_versions/v1.1], [https://www.gnu.org/copyleft/fdl.html GNU FDL v.1.3]  |- |-  |{{#if: {{{2|}}} | <span title="{{{2}}}" style="color:red;">Known problems</span> | &nbsp; }} |{{#if: {{{2|}}} | <span title="{{{2}}}" style="color:red;">Known problems</span> | &nbsp; }}  | |  |} |} Andrey.filippov

‎Python

← Older revision Revision as of 01:00, 19 July 2018 (One intermediate revision by the same user not shown)Line 44: Line 44:  * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only    −==<font color='ForestGreen'>TIFF stacks for ML</font>==+==<font color='ForestGreen'>TIFF image 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:Tiff layers.jpeg|thumb|400px|Fig.2 TIFF imagestack layers]] [[File:Tiff layers.jpeg|thumb|400px|Fig.2 TIFF imagestack layers]] Line 119: Line 119:    values data: (242, 324, 3)</font>   values data: (242, 324, 3)</font>    −[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing (actually, see the CVPR2018 presentation, p.23)]]+[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.5 Single layer packing (actually, see the CVPR2018 presentation, p.23)]]  '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> Oleg

‎Python

← Older revision Revision as of 01:00, 19 July 2018 (8 intermediate revisions by the same user not shown)Line 44: Line 44:  * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only * *.kml, rating.txt, thumb.jpeg - files, related to the online viewer only    −==<font color='ForestGreen'>TIFF stacks for ML</font>==+==<font color='ForestGreen'>TIFF image 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>    −[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing (actually, see the CVPR2018 presentation, p.23)]]+[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.5 Single layer packing (actually, see the CVPR2018 presentation, p.23)]]  '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> Oleg

‎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

‎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

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== Licensing ==
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‎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

‎TIFF stacks for ML

← Older revision Revision as of 20:13, 13 July 2018 (2 intermediate revisions by the same user not shown)Line 45: Line 45:     ==<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]]+[[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|800px|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]] Line 54: Line 54:  *** '''hor-pairs''' *** '''hor-pairs'''  *** '''vert-pairs''' *** '''vert-pairs''' −*** '''other''' - encoded values: estimated disparity, residual disparity and confidence for the residual disparity+*** '''other''' - encoded values: estimated disparity, estimated+residual disparity, and confidence for the residual disparity  * 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: Oleg

← Older revision Revision as of 19:19, 13 July 2018 (One intermediate revision by the same user not shown)Line 45: Line 45:     ==<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]]+[[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|800px|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]] Oleg

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== Licensing ==
{{CC }} Oleg

‎Python

← Older revision Revision as of 00:49, 13 July 2018 Line 110: Line 110:    values data: (242, 324, 3)</font>   values data: (242, 324, 3)</font>    −[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing]]+[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing (actually, see the CVPR2018 presentation, p.23)]]  '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> Oleg

‎Python

← Older revision Revision as of 00:49, 13 July 2018 (One intermediate revision by the same user not shown)Line 110: Line 110:    values data: (242, 324, 3)</font>   values data: (242, 324, 3)</font>    − +[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing (actually, see the CVPR2018 presentation, p.23)]]  '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> Oleg

‎Python

← Older revision Revision as of 20:20, 12 July 2018 Line 110: Line 110:    values data: (242, 324, 3)</font>   values data: (242, 324, 3)</font>    − +[[File:Ml tiff stack python tile packing.jpeg|thumb|400px|Fig.4 Single layer packing]]  '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: '''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> * <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font> Oleg

Oleg uploaded File:Ml tiff stack python tile packing.jpeg

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== Licensing ==
{{CC }} Oleg

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

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== Licensing ==
{{CC }} Oleg

← Older revision Revision as of 20:08, 12 July 2018 (2 intermediate revisions by the same user not shown)Line 60: Line 60:  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 - 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==== −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:  * <font color='DarkGreen'>'''Get tiff tags values (Pillow)'''</font> * <font color='DarkGreen'>'''Get tiff tags values (Pillow)'''</font>  * <font color='DarkGreen'>'''Parse Properties xml data stored by ImageJ in the tiff tags'''</font> * <font color='DarkGreen'>'''Parse Properties xml data stored by ImageJ in the tiff tags'''</font> Line 109: Line 109:    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>  +  +  +'''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  +* <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font>  + <font size=2>'''# The current packing is hardcoded in the script: (TY,TX,9,9,4) -> (TY,TX,100)'''  + # Get tiles from a tiff stack  + import pack_tile as pile  + packed_tiles = pile.pack(tile)  + # packed_tiles get stacked with '''estimated disparity''' (see '''test_nn_feed.py''')  + packed_tiles = np.dstack((packed_tiles,values[:,:,0])) Oleg

← Older revision Revision as of 20:08, 12 July 2018 (4 intermediate revisions by the same user not shown)Line 47: Line 47:  [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]]  [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-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]:  ** 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'''] Line 59: Line 60:  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 - 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==== −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:  * <font color='DarkGreen'>'''Get tiff tags values (Pillow)'''</font> * <font color='DarkGreen'>'''Get tiff tags values (Pillow)'''</font>  * <font color='DarkGreen'>'''Parse Properties xml data stored by ImageJ in the tiff tags'''</font> * <font color='DarkGreen'>'''Parse Properties xml data stored by ImageJ in the tiff tags'''</font> Line 104: Line 105:       −Upon opening tiff the image shape will be '''(height,width,layer)''' - for further processing it needs to be 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'>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>  +  +  +'''2.''' Use '''pack_tile.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to:  +* <font color='DarkGreen'>'''Pack image tiles for better structuring for ML'''</font>  + <font size=2>'''# The current packing is hardcoded in the script: (TY,TX,9,9,4) -> (TY,TX,100)'''  + # Get tiles from a tiff stack  + import pack_tile as pile  + packed_tiles = pile.pack(tile)  + # packed_tiles get stacked with '''estimated disparity''' (see '''test_nn_feed.py''')  + packed_tiles = np.dstack((packed_tiles,values[:,:,0])) Oleg

← Older revision Revision as of 23:19, 11 July 2018 (One intermediate revision by the same user not shown)Line 47: Line 47:  [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]] [[File:Ml tiff stack imagej.jpeg|thumb|400px|Fig.1 Opened in ImageJ]]  [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-layers]] [[File:Ml tiff stack python values.jpeg|thumb|800px|Fig.2 Decoded 'value'-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]:  ** 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'''] Line 104: Line 105:       −Upon opening tiff the image shape will be '''(height,width,layer)''' - for further processing it needs to be 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'>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