Sometimes it is nice to have a file of a specific size or pixel type for testing. To generate a file (that contains gradient images):
touch "my-special-test-file&pixelType=uint8&sizeX=8192&sizeY=8192.fake"
Whatever is before the & is the image name; remaining key value pairs should be pretty self-explanatory. Just replace the values with whatever you need for testing.
Additionally, you can put such values in a separate .ini file:
touch my-special-test-file.fake
echo "pixelType=uint8" >> my-special-test-file.fake.ini
echo "sizeX=8192" >> my-special-test-file.fake.ini
echo "sizeY=8192" >> my-special-test-file.fake.ini
In fact, just the .fake.ini file alone suffices:
echo "pixelType=uint8" >> my-special-test-file.fake
echo "sizeX=8192" >> my-special-test-file.fake
echo "sizeY=8192" >> my-special-test-file.fake
If you include a “[GlobalMetadata]” section to the ini file, then all the included values will be accessible from the global metadata map:
echo "[GlobalMetadata]" >> my-special-test-file.fake.ini
echo "my.key=some.value" >> my-special-test-file.fake.ini
There are a few other keys that can be added as well:
| Key | Value |
|---|---|
| thumbSizeX | number of pixels wide, for the thumbnail |
| thumbSizeY | number of pixels tall, for the thumbnail |
| physicalSizeX | real width of the pixels, supports units defaulting to microns |
| physicalSizeY | real height of the pixels, supports units defaulting to microns |
| physicalSizeZ | real depth of the pixels, supports units defaulting to microns |
| sizeZ | number of Z sections |
| sizeC | number of channels |
| sizeT | number of timepoints |
| bitsPerPixel | number of valid bits (<= number of bits implied by pixel type) |
| acquisitionDate | timestamp formatted as “yyyy-MM-dd_HH-mm-ss” |
| rgb | number of channels that are merged together |
| dimOrder | dimension order (e.g. XYZCT) |
| little | whether or not the pixel data should be little-endian |
| interleaved | whether or not merged channels are interleaved |
| indexed | whether or not a color lookup table is present |
| falseColor | whether or not the color lookup table is just for making the image look pretty |
| series | number of series (Images) |
| lutLength | number of entries in the color lookup table |
| exposureTime | time of exposure, supports units defaulting to seconds |
| plates | number of plates to generate |
| plateAcqs | number of plate runs |
| plateRows | number of rows per plate |
| plateCols | number of rows per plate |
| fields | number of fields per well |
| annLong, annDouble, annMap, annComment, annBool, annTime, annTag, annTerm, annXml | number of annotations of the given type to generate |
You can often work with the .fake file directly, but in some cases support for those files is disabled and so you will need to convert the file to something else. Make sure that you have Bio-Formats built and the JARs in your CLASSPATH (individual JARs or just bioformats_package.jar):
bfconvert test&pixelType=uint8&sizeX=8192&sizeY=8192.fake test.tiff
If you do not have the command line tools installed, substitute loci.formats.tools.ImageConverter for bfconvert.