Similar to spacetx/sptx-format#22, "tests" shows up as a top-level entity in site-packages.

$ pip uninstall slicedimage
Uninstalling slicedimage-0.0.6:
  Would remove:
    /lifesci/groups/jrs/jamoore/miniconda2/envs/starfish/bin/slicedimage
    /lifesci/groups/jrs/jamoore/miniconda2/envs/starfish/lib/python3.6/site-packages/slicedimage-0.0.6.dist-info/*
    /lifesci/groups/jrs/jamoore/miniconda2/envs/starfish/lib/python3.6/site-packages/slicedimage/*
    /lifesci/groups/jrs/jamoore/miniconda2/envs/starfish/lib/python3.6/site-packages/tests/*

Caveat emptor: I might be doing something wrong with ImageStack.

I'm cutting out some pieces of ImageStacks to produce smaller testing data. As far as I can tell, the only way to subset the ImageStack (e.g. as one might when cropping) is to access the private variable. If you then write to disk, it appears to write the old, uncropped data.

... which I guess makes sense, as this is a private variable, but it would be nice if this had cropping support.

A runtime check for the 2d image size would fix this, but I leave open the general problem (also relevant for starfish of how to deal with change sizes throughout processing. As it stands, ImageStack is acting strangely read-only.

When we figure out our dependency structure, we should include in a CONTRIBUTING.md file the SOP for incrementing slicedimage so that starfish can depend on it.

I tried using starfish on a MERFISH image with Z = 4, C = 2 (4 depth planes and 2 fluorophore channels).
First I used the function write_experiment_json(), to seperate the image to 8 different images and create the relevant JSON. The JSON states the shapes corretly to be (2048, 2048).

Next, when running Stack.from_experiment_json() and pointing to experiment.json, I get the error
"ValueError: Starfish does not support tiles that are not identical in shape".
The size of tile.tile_shape is (2048, 2048), but the size of self._tile_shape (coming from slicedimage) is (8, 2048, 2048).

I'm attaching the resulted hybridisation
hybridization-fov_000.txt

JSON, and happy to supply any other needed information.
Many thanks,
Eyal.

For example, in the following file structure:

experiment.json
fov_001/
  hybridization.json/
  file_0.tiff

The file path to file_0.tiff in hybridization.json needs to be fov_001/file_0.tiff not file_0.tiff, which is counter-intuitive.

The below code reproduces this issue -- it loads, but contains the odd file paths suggested above.

experiment = Experiment()
experiment.read('http://czi.starfish.data.public.s3.amazonaws.com/20180813/MERFISH/experiment.json')

slicedimage should outsource validation to sptx-formats, allowing us to keep any refactoring of spec-related changes to one place.

ACs:

• slicedimage imports sptx-format
• all validation occurs in imported tool.

We want to be able to check if the data has been downloaded locally before we load the imagestack. If it exists, we want to use the local copy in lieu of a web link.

Slicedimage needs to be able to read Numpy files.

• The spec says we support it.
• We write numpy files.

Do it after #29 lands

• #13
• #14
• #15
• #16

from an offline chat... here's a set of nouns to explain the basic concepts underlying the data structure here

general concept

A collection of images is specified by a JSON file. A collection consists of multiple tilesets, each of which is also specified by a JSON file. A tileset consists of multiple tiles.

|- collection (collection.json)
  |- tileset (tileset1.json)
	|- tile 
	|- tile
	|- tile
  |- tileset (tileset2.json)
	|- tile
  |- tileset (tileset3.json)
	|- tile
	|- tile

worked example

A collection is an experiment / hybridization, for each experiment we have multiple fields of view, for each field of view we have multiple tiles.

|- hybridization.json
  |- hybridization_fov_000.json
    |- image0.tif
    |- image1.tif
    |- ... 
  |- hybridization_fov_001.json
    |- image0.tif
    |- image1.tif
    |- ...

Related to spacetx/starfish#917

I was trying to use these to crop and found it difficult to understand what was going on without reading all the source code.

Additional point of confusion: it would be awesome if TileSet (via delegation to Tile, perhaps) could have a read and write methods, instead of going through an external Reader class.

Ideally I'd like to be able to read the TileSet, manipulate it, and then dump it to disk. I struggled to accomplish this without writing janky new code.

sptx-format should move into starfish.

The BICCN is storing image data at the Brain Image Library and BIL's current approaches for raw image data access are

• anonymous FTP for public access once image data has been published
• authenticated methods with shell access for users for in-process/unpublished data

An anonymous FTP backend for slicedimage would allow users to load published BIL data locally and some authenticated method would allow the same kind of access for unpublished data on BIL.

@ttung per our slack conversation and @ambrosejcarr just in case you're interested

@kevinyamauchi needs this.