Mercurial > repos > iuc > imagej2_bunwarpj_raw_transform

annotate jython_utils.py @ 0:64aacdf3171f draft

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planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
author iuc
date Fri, 19 Jun 2015 16:59:58 -0400
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children 6f129c1ec6d1
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64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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1 import imagej2_base_utils
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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2 from ij import IJ
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3
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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4 def convert_before_saving_as_tiff( image_plus ):
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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5 # The bUnwarpJ plug-in produces TIFF image stacks consisting of 3
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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6 # slices which can be viewed in ImageJ. The 3 slices are: 1) the
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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7 # registered image, 2) the target image and 3) the black/white warp
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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8 # image. When running bUnwarpJ from the command line (as these
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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9 # Galaxy wrappers do) the initial call to IJ.openImage() (to open the
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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10 # registered source and target images produced by bUnwarpJ) in the
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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11 # tool's jython_script.py returns an ImagePlus object with a single
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
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12 # slice which is the "generally undesired" slice 3 discussed above.
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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13 # However, a call to IJ.saveAs() will convert the single-slice TIFF
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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14 # into a 3-slice TIFF image stack (as described above) if the selected
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15 # format for saving is TIFF. Galaxy supports only single-layered
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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16 # images, so to work around this behavior, we have to convert the
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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17 # image to something other than TIFF so that slices are eliminated.
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18 # We can then convert back to TIFF for saving. There might be a way
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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19 # to do this without converting twice, but I spent a lot of time looking
64aacdf3171f planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
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20 # and I have yet to discover it.
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21 tmp_dir = imagej2_base_utils.get_temp_dir()
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22 tmp_out_png_path = imagej2_base_utils.get_temporary_image_path( tmp_dir, 'png' )
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23 IJ.saveAs( image_plus, 'png', tmp_out_png_path )
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24 return IJ.openImage( tmp_out_png_path )