‎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

Oleg Dzhimiev committed changes to the Elphel git project :
NaNs are already taken care of

‎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

Oleg Dzhimiev committed changes to the Elphel git project :
tested

Oleg Dzhimiev committed changes to the Elphel git project :
added NaNs

Oleg Dzhimiev committed changes to the Elphel git project :
simplified packing, next test

Oleg Dzhimiev committed changes to the Elphel git project :
fixed packing to 4x faster

AndreyFilippov committed changes to the Elphel git project :
Using main camera -only DSI in the model where aux camera is occluded

← 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

‎TIFF stacks for ML

← Older revision Revision as of 22:50, 11 July 2018 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'''] Oleg

Oleg uploaded File:Ml tiff stack python data layers.jpeg

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== Licensing ==
{{CC }} Oleg

‎Python

← Older revision Revision as of 22:44, 11 July 2018 (4 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 python values.jpeg|thumb|800px|Fig.2 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]: * 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 58: Line 60:  ====Python==== ====Python====  Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: Use '''imagej_tiff.py''' from [https://git.elphel.com/Elphel/python3-imagej-tiff python3-imagej-tiff] to: −* get tiff tags values (Pillow)+* <font color='DarkGreen'>'''Get tiff tags values (Pillow)'''</font> −* parse Properties xml data stored in the tiff tags used by ImageJ+* <font color='DarkGreen'>'''Parse Properties xml data stored by ImageJ in the tiff tags'''</font> −* get tile dimensions from Properties+* <font color='DarkGreen'>'''Get tiles dimensions from Properties'''</font> −* read layers as numpy arrays for further computations or plotting+* <font color='DarkGreen'>'''Convert layers to numpy arrays (split into tiles or optionally not split) for further computations and plotting'''</font> −Example:+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;'>'''~$ python3 imagej_tiff.py 1527256903_350165-ML_DATA-08B-O-FZ0.05-OFFS0.00000.tiff'''    time: 1531344391.7055812   time: 1531344391.7055812 Oleg

Oleg uploaded File:Ml tiff stack python values.jpeg

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== Licensing ==
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Oleg uploaded File:Ml tiff stack imagej.jpeg

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== Licensing ==
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Oleg Dzhimiev committed changes to the Elphel git project :
still testing