-The export step is handled through the data export applet in ilastik. In [pixel classification]({{baseurl}}/documentation/pixelclassification/pixelclassification.html), for example, the applet is called "Prediction Export".
+The export step is handled through the data export applet in ilastik. In [pixel classification]({{baseurl}}/documentation/pixelclassification/pixelclassification.html), for example, the applet is called "Prediction Export".
The GUI can be used to change export settings as well as to bulk export all of the data. The following controls are available in the panel:
* **Source:** offers a drop-down menu of layers which can be exported. For example, in [pixel classification]({{baseurl}}/documentation/pixelclassification/pixelclassification.html) you can export label probabilities or segmentations.
@@ -55,7 +55,7 @@ On the right you can see all your datasets listed by their nickname, as defined
- *Renormalize \[min,max\] from:* Use this setting to scale the range of your results. For example, prediction data is typically given a range of \[0.0,1.0\], but you can scale it to the range of \[0,255\] for easy viewing with other software.
- *Transpose to Axis Order:* This setting sets "outermost" and "innermost" axes (and so on). For some formats, this doesn't matter so much (e.g. hdf5). For others, you may care. For example, when exporting a stack of pngs across the Z dimension, make sure 'z' appears on the left (the outer dimension). If you aren't sure, tzyxc is typically a good choice.
-**Note:** if you export probability maps (pixelwise prediction results) and want to view them in other software, **convert them to data type "integer 8-bit"** and check the "Renormalize" check box to change the range.
+**Note:** if you export probability maps (pixelwise prediction results) and want to view them in other software, **convert them to data type "integer 8-bit"** and check the "Renormalize" check box to change the range.
- **Output File Info:** Use these controls to select an output file format and location. A few _"magic" placeholders_ can be used in these settings. These are useful when you are exporting multiple datasets:
- `{dataset_dir}` - the directory containing the original raw dataset
@@ -65,7 +65,7 @@ On the right you can see all your datasets listed by their nickname, as defined
- `{x_start}`, `{x_stop}`, `{y_start}`, `{y_stop}`, etc - Specific axis start/stop boundaries for the region-of-interest
- `{slice_index}` - The index of each slice in an exported image sequence (required for all image sequence formats, not allowed with any other format).
-- **Exporting sequences:** When a 3D, 4D or 5D dataset is exported as a sequence, ilastik chooses the first axis as the slicing one. For example, if your dataset is 1001x1002x1003 pixels and you choose to export it as an image sequence, it will export 1001 images, 1002x1003 pixels each. This information is displayed in the dialogue if you select a "sequence" output format. To change the slicing axis, use the "Transpose to Axis Order" control to bring the axis you need to the front. Continuing on the 1001x1002x1003 example, assume it had "xyz" as axis order. Now if you want to slice on the z axis (of size 1003), type "zxy" in the "Transpose to Axis Order" control. Now ilastik will export 1003 images, 1001x1002 pixels each.
+- **Exporting sequences:** When a 3D, 4D or 5D dataset is exported as a sequence, ilastik chooses the first axis as the slicing one. For example, if your dataset is 1001x1002x1003 pixels and you choose to export it as an image sequence, it will export 1001 images, 1002x1003 pixels each. This information is displayed in the dialogue if you select a "sequence" output format. To change the slicing axis, use the "Transpose to Axis Order" control to bring the axis you need to the front. Continuing on the 1001x1002x1003 example, assume it had "xyz" as axis order. Now if you want to slice on the z axis (of size 1003), type "zxy" in the "Transpose to Axis Order" control. Now ilastik will export 1003 images, 1001x1002 pixels each.