wipp-plugin.json

{
	"name": "MIST",
	"version": "2.0.7",
	"title": "MIST plugin",
	"author": "Michael Majurski and Tim Blattner",
	"institution": "National Institute of Standards and Technology",
	"repository": "https://github.com/usnistgov/MIST",
	"website": "https://isg.nist.gov/deepzoomweb/resources/csmet/pages/image_stitching/image_stitching.html",
	"citation": "Chalfoun, Joe, et al. \"Mist: accurate and scalable microscopy image stitching tool with stage modeling and error minimization.\" Scientific reports (2017)",
	"description": "Microscopy Image Stitching Tool",
	"containerId": "wipp/mist:2.0.7",

	"inputs": [
		{
			"name": "imageDir",
			"type": "collection",
            "options": {
				"format": "tiledtiff"
			},
			"description": "Input Images",
            "required": true
		},
        {
			"name": "filenamePatternType",
			"type": "enum",
			"options": {
				"values": [
					"ROWCOL",
                    "SEQUENTIAL"
				]
			},
			"description": "Filename Pattern Type",
            "required": true
		},
        {
			"name": "filenamePattern",
			"type": "string",
			"description": "Filename Pattern",
            "required": true
		},
        {
			"name": "gridOrigin",
			"type": "enum",
			"options": {
				"values": [
					"UL",
                    "UR",
                    "LL",
                    "LR"
				]
			},
			"description": "Starting Point"
		},
        {
			"name": "numberingPattern",
			"type": "enum",
			"options": {
				"values": [
					"VERTICALCOMBING",
                    "VERTICALCONTINUOUS",
                    "HORIZONTALCOMBING",
                    "HORIZONTALCONTINUOUS"
				]
			},
			"description": "Direction"
		},
        {
			"name": "gridWidth",
			"type": "number",
			"description": "Grid Width",
            "required": true
		},
        {
			"name": "gridHeight",
			"type": "number",
			"description": "Grid Height",
            "required": true
		},
        {
			"name": "startTile",
			"type": "enum",
			"options": {
				"values": [
					"0",
					"1"
				]
			},
			"description": "Start tile"
		},
        {
			"name": "startTileRow",
			"type": "enum",
			"options": {
				"values": [
					"0",
					"1"
				]
			},
			"description": "Start tile row"
		},
        {
			"name": "startTileCol",
			"type": "enum",
			"options": {
				"values": [
					"0",
					"1"
				]
			},
			"description": "Start tile column"
		},
        {
			"name": "startRow",
			"type": "number",
			"description": "Subgrid start row"
		},
        {
			"name": "startCol",
			"type": "number",
			"description": "Subgrid start column"
		},
        {
			"name": "extentWidth",
			"type": "number",
            "bind": "gridWidth",
			"description": "Subgrid extent width"
		},
        {
			"name": "extentHeight",
			"type": "number",
            "bind": "gridHeight",
			"description": "Subgrid extent height"
		},
        {
			"name": "isTimeSlices",
			"type": "boolean",
			"description": "Has timeslices"
		},
        {
			"name": "timeSlices",
			"type": "string",
			"description": "Timeslices"
		},
		{
	      "name": "assembleNoOverlap",
	      "type": "enum",
				"options": {
					"values": [
						"False",
	                    "True"
					]
				},
	      "description": "Whether or not to assemble images without overlap.",
	      "required": true
	    },
        {
			"name": "stageRepeatability",
			"type": "number",
			"description": "Stage repeatability"
		},
        {
			"name": "horizontalOverlap",
			"type": "number",
			"description": "Horizontal Overlap"
		},
        {
			"name": "verticalOverlap",
			"type": "number",
			"description": "Vertical Overlap"
		},
        {
			"name": "overlapUncertainty",
			"type": "number",
			"description": "Overlap Uncertainty"
		},
        
		{
			"name": "programType",
			"type": "enum",
			"options": {
				"values": [
					"JAVA",
					"FFTW",
					"CUDA"
				]
			},
			"description": "Stitching Program"
		}
        
        
        
		
	],
	"outputs": [
		{
			"name": "outputPath",
			"type": "stitchingVector",
			"description": "Output stitching vector"
		}
	],
	"ui": [
		{
	      "key": "inputs.assembleNoOverlap",
	      "title": "Assemble No Overlap: ",
	      "description": "Whether or not to assemble images with no overlap."
	    },
    	{
			"key": "inputs.imageDir",
			"title": "Input Images: ",
			"description": "Pick a collection..."
		},
        {
			"key": "inputs.filenamePatternType",
			"title": "Filename Pattern Type: ",
			"description": "Specify the type of filename pattern used in the acquired images."
		},
        {
			"key": "inputs.filenamePattern",
			"title": "Filename Pattern: ",
			"description": "Specify the filename pattern."
		},
        {
			"key": "inputs.gridOrigin",
			"title": "Starting Point: ",
			"description": "Specify the starting point of the microscope scan, specifies the origin for the grid of images."
		},
        {
			"key": "inputs.numberingPattern",
			"title": "Direction: ",
			"description": "Specify the direction and pattern of the microscope motion during acquisition.",
            "condition": "model.inputs.filenamePatternType=='SEQUENTIAL'"
		},
        {
			"key": "inputs.gridWidth",
			"title": "Grid Width: ",
			"description": "Specify the number of images in a row (The number of columns, the width of the image grid)."
		},
        {
			"key": "inputs.gridHeight",
			"title": "Grid Height: ",
			"description": "Specify the number of images in a column. (The number of rows, the height of the image grid)."
		},
        {
			"key": "inputs.startTile",
			"title": "Start Tile: ",
			"description": "Specify the index of the first tile (0 or 1)",
            "condition": "model.inputs.filenamePatternType=='SEQUENTIAL'"
		},
        {
			"key": "inputs.startTileRow",
			"title": "Start Tile Row: ",
			"description": "Specify the index of the first tile row (0 or 1)",
            "condition": "model.inputs.filenamePatternType=='ROWCOL'"
		},
        {
			"key": "inputs.startTileCol",
			"title": "Start Tile Column: ",
			"description": "Specify the index of the first tile column (0 or 1)",
            "condition": "model.inputs.filenamePatternType=='ROWCOL'"
		},
        {
			"key": "inputs.startRow",
			"title": "Subgrid Start Row: ",
			"description": "Specify the start row for the subgrid",
            "hidden": true,
            "default": 0
		},
        {
			"key": "inputs.startCol",
			"title": "Subgrid Start Column: ",
			"description": "Specify the start column for the subgrid",
            "hidden": true,
            "default": 0
		},
        {
			"key": "inputs.extentWidth",
			"title": "Subgrid Extent Width: ",
			"description": "Specify the width for the subgrid",
            "hidden": true,
            "bind": "gridWidth"
		},
        {
			"key": "inputs.extentHeight",
			"title": "Subgrid Extent Height: ",
			"description": "Specify the height for the subgrid",
            "hidden": true,
            "bind": "gridHeight"
		},
        {
			"key": "inputs.isTimeSlices",
			"title": "Has timeslices: ",
			"description": "Specify if the dataset has timeslices.",
            "default": true
		},
        {
			"key": "inputs.timeSlices",
			"title": "Timeslices: ",
			"description": "Specify the timeslices to stitch",
            "condition": "model.inputs.isTimeSlices==true"
		},
        {
			"key": "inputs.stageRepeatability",
			"title": "Stage Repeatability: ",
			"description": "Specify the stage repeatability variable used when computing the global optimization",
            "default": 0,
            "condition": "model.inputs.assembleNoOverlap=='False'"
		},
        {
			"key": "inputs.horizontalOverlap",
			"title": "Horizontal Overlap: ",
			"description": "Specify the horizontal overlap variable used when computing the global optimization",
            "condition": "model.inputs.assembleNoOverlap=='False'"
		},
        {
			"key": "inputs.verticalOverlap",
			"title": "Vertical Overlap: ",
			"description": "Specify the vertical overlap variable when computing the global optimization",
            "condition": "model.inputs.assembleNoOverlap=='False'"
		},
        {
			"key": "inputs.overlapUncertainty",
			"title": "Overlap Uncertainty: ",
			"description": "Specify the overlap uncertainty variable when computing the global optimization",
             "default": 5,
            "condition": "model.inputs.assembleNoOverlap=='False'"
		},
        
        
        {
			"key": "inputs.programType",
			"title": "Stitching Program: ",
			"description": "Select which type of program to execute.",
            "condition": "model.inputs.assembleNoOverlap=='False'"
		},
        {
            "key" : "fieldsets",
            "fieldsets": [
                {
                  "title": "Input images",
                  "fields": [
                  	"assembleNoOverlap",
                    "imageDir",
                    "filenamePatternType",
                    "filenamePattern"
                  ]
                },
                {
                  "title": "Acquisition setup",
                  "fields": [
                    "gridOrigin",
                    "numberingPattern",
                    "gridWidth",
                    "gridHeight",
                    "startTile",
                    "startTileRow",
                    "startTileCol",
                    "isTimeSlices",
                    "timeSlices"
                  ]
                },
                {
                  "title": "Advanced parameters",
                  "fields": [
                    "startRow",
                    "startCol",
                    "extentWidth",
                    "extentHeight",
                    "stageRepeatability",
                    "horizontalOverlap",
                    "verticalOverlap",
                    "overlapUncertainty",
                    "programType"
                  ]
                }
            ]
        }
	]
}