help > Execute App2 from command line on directory of 2d tif images (image series)
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Apr 9, 2020  11:04 AM | Matt Mallory
Execute App2 from command line on directory of 2d tif images (image series)
Hello,

I was wondering if there is a way to run app2 from command line that will execute neuron tracing on a directory of 2d tif images, that when stacked together will construct the 3d neuron of interest. The script will not run if a .tif image is not given in the /i parameter. (Windows 10 user, Vaa3d v3.475)

Alternatively, is there a command line functionality in Vaa3d that creates an image stack from an image series?

Thank you,

Matt
May 5, 2020  10:05 AM | Hanchuan Peng
RE: Execute App2 from command line on directory of 2d tif images (image series)
Yes, you can import a series of image sections and save as a 3D tiff stack. Check the 'import' function in main menu.

No, we do not support running APP2 for the 2D folder. The code is there, you may write a wrapper to load data first followed by APP2 tracing.


Originally posted by Matt Mallory:
Hello,

I was wondering if there is a way to run app2 from command line that will execute neuron tracing on a directory of 2d tif images, that when stacked together will construct the 3d neuron of interest. The script will not run if a .tif image is not given in the /i parameter. (Windows 10 user, Vaa3d v3.475)

Alternatively, is there a command line functionality in Vaa3d that creates an image stack from an image series?

Thank you,

Matt
May 11, 2020  10:05 AM | Matt Mallory
RE: Execute App2 from command line on directory of 2d tif images (image series)
Hello,

Thank you for the detailed response. I am trying to use Fiji to convert my 2D folder of tif images into a .v3draw file so that there are no tiff formatting issues when loading into vaa3d. In Fiji I load the image directory as a virtual stack and then just export as .v3draw file.
However, when I use this v3draw file with vaa3d app2, I am now getting an error as shown below.

I was wondering how can I fix this issue?

The current input file has the suffix [v3draw]
The data does not have supported image file suffix, -- now this program assumes it is Vaa3D's RAW format and tries to load it...

size of [V3DLONG]=[8], [V3DLONG]=[8] [int]=[4], [short int]=[2], [double]=[8], [float]=[4]
The data endian code is
The machine endian code is [L]
machine endian=[L] data endian=[b] b_swap=1
mysz raw read unit[0]: [-2145583104] swap unit: [7552][1d80]
mysz raw read unit[1]: [-2145583104] swap unit: [7552][1d80]
mysz raw read unit[2]: [1023541248] swap unit: [573][23d]
mysz raw read unit[3]: [16777216] swap unit: [1][1]
Fail to allocate memory in loadRaw2Stack().
The data doesn't look like a correct 4-byte-size Vaa3D's RAW file. Try 2-byte-raw.
The size of your input file is too small and is not correct, -- it is too small to contain the legal header.
Error happens in reading 4-byte-size and 2-byte-size Vaa3D's RAW file. Stop.
[/b]
May 11, 2020  11:05 AM | Matt Mallory
RE: Execute App2 from command line on directory of 2d tif images (image series)
Actually was able to load the image, however when trying to run app2 it fails as seen below. I get a memory error with My4DImageSimple, and the v3draw image is only 31GB. I have the 128Gb iunstalled RAM. What memory is this error referencing?



Just read 2147483646 units, each unit has the size = 1
Finish reading 6.5713%
Just read 2147483646 units, each unit has the size = 1
Finish reading 13.1426%
Just read 2147483646 units, each unit has the size = 1
Finish reading 19.7139%
Just read 2147483646 units, each unit has the size = 1
Finish reading 26.2852%
Just read 2147483646 units, each unit has the size = 1
Finish reading 32.8565%
Just read 2147483646 units, each unit has the size = 1
Finish reading 39.4278%
Just read 2147483646 units, each unit has the size = 1
Finish reading 45.9991%
Just read 2147483646 units, each unit has the size = 1
Finish reading 52.5704%
Just read 2147483646 units, each unit has the size = 1
Finish reading 59.1417%
Just read 2147483646 units, each unit has the size = 1
Finish reading 65.7130%
Just read 2147483646 units, each unit has the size = 1
Finish reading 72.2843%
Just read 2147483646 units, each unit has the size = 1
Finish reading 78.8556%
Just read 2147483646 units, each unit has the size = 1
Finish reading 85.4269%
Just read 2147483646 units, each unit has the size = 1
Finish reading 91.9982%
Just read 2147483646 units, each unit has the size = 1
Finish reading 98.5695%
Just read 467484702 units, each unit has the size = 1
Finish reading 100%
unable to open marker file []
start to preprocessing.

Fail to allocate memory in My4DImageSimple::createImage();
May 13, 2020  08:05 PM | Hanchuan Peng
RE: Execute App2 from command line on directory of 2d tif images (image series)
It does not seem to be a good idea to allocate memory for a 30+GB image and then try to generate a graph as specified in APP2, a 128GB memory won't be a cure. Indeed I would suggest you run APP2 for smaller trunks of the data, or use sth like UltraTracer to solve the problem in divide-and-conquer way.




Originally posted by Matt Mallory:
Actually was able to load the image, however when trying to run app2 it fails as seen below. I get a memory error with My4DImageSimple, and the v3draw image is only 31GB. I have the 128Gb iunstalled RAM. What memory is this error referencing?



Just read 2147483646 units, each unit has the size = 1
Finish reading 6.5713%
Just read 2147483646 units, each unit has the size = 1
Finish reading 13.1426%
Just read 2147483646 units, each unit has the size = 1
Finish reading 19.7139%
Just read 2147483646 units, each unit has the size = 1
Finish reading 26.2852%
Just read 2147483646 units, each unit has the size = 1
Finish reading 32.8565%
Just read 2147483646 units, each unit has the size = 1
Finish reading 39.4278%
Just read 2147483646 units, each unit has the size = 1
Finish reading 45.9991%
Just read 2147483646 units, each unit has the size = 1
Finish reading 52.5704%
Just read 2147483646 units, each unit has the size = 1
Finish reading 59.1417%
Just read 2147483646 units, each unit has the size = 1
Finish reading 65.7130%
Just read 2147483646 units, each unit has the size = 1
Finish reading 72.2843%
Just read 2147483646 units, each unit has the size = 1
Finish reading 78.8556%
Just read 2147483646 units, each unit has the size = 1
Finish reading 85.4269%
Just read 2147483646 units, each unit has the size = 1
Finish reading 91.9982%
Just read 2147483646 units, each unit has the size = 1
Finish reading 98.5695%
Just read 467484702 units, each unit has the size = 1
Finish reading 100%
unable to open marker file []
start to preprocessing.

Fail to allocate memory in My4DImageSimple::createImage();
May 20, 2020  01:05 PM | Matt Mallory
RE: Execute App2 from command line on directory of 2d tif images (image series)
Hello Hanchuan,

Thank you for the information. I'm a bit confused though why this tracing will not work from command line, but I am able to use app2 with user interface. I would expect the command line use to be faster and able to trace the same images that can be done with user interface?

Thank you,
Matt