cdeepakroy
commented
8 years ago Below is a sample POST request that runs a CLI that does ColorDeconvolution
api/v1/HistomicsTK/ColorDeconvolution/run?itemId=56279eb3a8487354347916c6&folderId=56279ecea8487354347916cd&stainColor_1=%5B0.65%2C%200.70%2C%200.29%5D&stainColor_2=%5B0.07%2C%200.99%2C%200.11%5D&stainColor_3=%5B0%2C%200%2C%200%5D
and below is the response:
{
"_accessLevel": 2,
"_id": "56cf65fba8487359caad8382",
"_modelType": "job",
"args": [],
"async": false,
"celeryTaskId": "f09e40be-306d-49e8-8feb-8807122f1dfc",
"created": "2016-02-25T20:37:15.682372+00:00",
"interval": 0,
"kwargs": {
"auto_convert": true,
"cleanup": true,
"inputs": {
"inputImageFile": {
"format": "string",
"host": "localhost",
"id": "56279eb3a8487354347916c6",
"mode": "girder",
"name": "A.png",
"port": 8080,
"resource_type": "item",
"token": "8kFFXZqZfajQU4yuVvKnz0hgqfEG4mw4vSRe71QO6ZWselKZXnZFjRDiEZlX3HXh",
"type": "string"
},
"stainColor_1": {
"data": "[0.65, 0.70, 0.29]",
"format": "json",
"mode": "inline",
"type": "number_list"
},
"stainColor_2": {
"data": "[0.07, 0.99, 0.11]",
"format": "json",
"mode": "inline",
"type": "number_list"
},
"stainColor_3": {
"data": "[0, 0, 0]",
"format": "json",
"mode": "inline",
"type": "number_list"
}
},
"jobInfo": {
"headers": {
"Girder-Token": "CTlsh1TOxaVtOGTQgX0QyC5FLlU9KF2hPv9N5t72z44iuFw7wreGnmVesa9c4AIq"
},
"logPrint": true,
"method": "PUT",
"url": "http://localhost:8080/api/v1/job/56cf65fba8487359caad8382"
},
"outputs": {
"outputStainImageFile_1": {
"format": "string",
"host": "localhost",
"mode": "girder",
"name": "A_stain_1.png",
"parent_id": "56279ecea8487354347916cd",
"parent_type": "folder",
"port": 8080,
"resource_type": "item",
"token": "8kFFXZqZfajQU4yuVvKnz0hgqfEG4mw4vSRe71QO6ZWselKZXnZFjRDiEZlX3HXh",
"type": "string"
},
"outputStainImageFile_2": {
"format": "string",
"host": "localhost",
"mode": "girder",
"name": "A_stain_2.png",
"parent_id": "56279ecea8487354347916cd",
"parent_type": "folder",
"port": 8080,
"resource_type": "item",
"token": "8kFFXZqZfajQU4yuVvKnz0hgqfEG4mw4vSRe71QO6ZWselKZXnZFjRDiEZlX3HXh",
"type": "string"
},
"outputStainImageFile_3": {
"format": "string",
"host": "localhost",
"mode": "girder",
"name": "A_stain_3.png",
"parent_id": "56279ecea8487354347916cd",
"parent_type": "folder",
"port": 8080,
"resource_type": "item",
"token": "8kFFXZqZfajQU4yuVvKnz0hgqfEG4mw4vSRe71QO6ZWselKZXnZFjRDiEZlX3HXh",
"type": "string"
}
},
"task": {
"inputs": [
{
"format": "string",
"id": "inputImageFile",
"target": "filepath",
"type": "string"
},
{
"format": "number_list",
"id": "stainColor_1",
"type": "number_list"
},
{
"format": "number_list",
"id": "stainColor_2",
"type": "number_list"
},
{
"default": {
"data": [
0,
0,
0
],
"format": "number_list"
},
"format": "number_list",
"id": "stainColor_3",
"type": "number_list"
}
],
"mode": "python",
"name": "ColorDeconvolution",
"outputs": [
{
"format": "string",
"id": "outputStainImageFile_1",
"target": "filepath",
"type": "string"
},
{
"format": "string",
"id": "outputStainImageFile_2",
"target": "filepath",
"type": "string"
},
{
"format": "string",
"id": "outputStainImageFile_3",
"target": "filepath",
"type": "string"
}
],
"script": "import os\nimport numpy as np\nimport skimage.io\nimport histomicstk as htk\n\n# Define Romanesco globals for the style checker\ninputImageFile = inputImageFile # noqa\nstainColor_1 = stainColor_1 # noqa\nstainColor_2 = stainColor_2 # noqa\nstainColor_3 = stainColor_3 # noqa\n_tempdir = _tempdir # noqa\n\n# Read Input Image\nprint('>> Reading input image')\n\nprint(inputImageFile)\n\ninputImage = skimage.io.imread(inputImageFile)\n\n# Create stain matrix\nprint('>> Creating stain matrix')\n\nW = np.array([stainColor_1, stainColor_2, stainColor_3]).T\nprint W\n\n# Perform color deconvolution\nprint('>> Performing color deconvolution')\nres = htk.ColorDeconvolution(inputImage, W)\n\n# write stain images to output\nprint('>> Outputting individual stain images')\noutFileSuffix = os.path.split(inputImageFile)[1]\n\noutputStainImageFile_1 = os.path.join(_tempdir, 'stain_1_' + outFileSuffix)\nskimage.io.imsave(outputStainImageFile_1, res.Stains[:, :, 0])\n\noutputStainImageFile_2 = os.path.join(_tempdir, 'stain_2_' + outFileSuffix)\nskimage.io.imsave(outputStainImageFile_2, res.Stains[:, :, 1])\n\noutputStainImageFile_3 = os.path.join(_tempdir, 'stain_3_' + outFileSuffix)\nskimage.io.imsave(outputStainImageFile_3, res.Stains[:, :, 2])\n"
},
"validate": false
},
"log": "",
"meta": {},
"progress": null,
"public": false,
"status": 1,
"timestamps": [
{
"status": 1,
"time": "2016-02-25T20:37:15.811107+00:00"
}
],
"title": "ColorDeconvolution",
"type": "ColorDeconvolution",
"updated": "2016-02-25T20:37:15.811107+00:00",
"when": "2016-02-25T20:37:15.682372+00:00"
}
The front end should have ways to: