root/Xml/Working/CLI.xsd
| Revision 195, 28.5 kB (checked in by andrew, 4 months ago) |
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| 1 | <?xml version = "1.0" encoding = "UTF-8"?> |
| 2 | <!-- |
| 3 | #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| 4 | # |
| 5 | # Copyright (C) 2003-2008 Open Microscopy Environment |
| 6 | # Massachusetts Institute of Technology, |
| 7 | # National Institutes of Health, |
| 8 | # University of Dundee, |
| 9 | # University of Wisconsin at Madison |
| 10 | # |
| 11 | #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| 12 | --> |
| 13 | <!-- |
| 14 | #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| 15 | # Written by: Josiah Johnston <siah@nih.gov>, Andrew J Patterson |
| 16 | #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| 17 | --> |
| 18 | <xsd:schema xmlns:xsd = "http://www.w3.org/2001/XMLSchema" |
| 19 | targetNamespace = "http://www.openmicroscopy.org/Schemas/CLI/2008-02" |
| 20 | xmlns:CLI = "http://www.openmicroscopy.org/Schemas/CLI/2008-02" |
| 21 | xmlns:xml="http://www.w3.org/XML/1998/namespace" |
| 22 | version = "1" |
| 23 | elementFormDefault = "qualified"> |
| 24 | <xsd:import namespace="http://www.w3.org/XML/1998/namespace" schemaLocation="http://www.w3.org/2001/xml.xsd"/> |
| 25 | <xsd:annotation> |
| 26 | <xsd:documentation> |
| 27 | Open Microscopy Environment |
| 28 | Command Line Interface XML Schema |
| 29 | Author: Josiah Johnston, Andrew J Patterson |
| 30 | </xsd:documentation> |
| 31 | </xsd:annotation> |
| 32 | <xsd:attributeGroup name = "InputLocation"> |
| 33 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 34 | <xsd:annotation> |
| 35 | <xsd:documentation>This specifies where to find a piece of data by FormalInputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Input 'foo', Location="foo.bar" </xsd:documentation> |
| 36 | </xsd:annotation> |
| 37 | </xsd:attribute> |
| 38 | </xsd:attributeGroup> |
| 39 | <xsd:attributeGroup name = "OutputLocation"> |
| 40 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 41 | <xsd:annotation> |
| 42 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 43 | </xsd:annotation> |
| 44 | </xsd:attribute> |
| 45 | </xsd:attributeGroup> |
| 46 | <xsd:element name = "ExecutionInstructions"> <!-- top level definition --> |
| 47 | <xsd:annotation> |
| 48 | <xsd:documentation>Tied to DB. Table PROGRAMS Column EXECUTION |
| 49 | </xsd:documentation> |
| 50 | </xsd:annotation> |
| 51 | <xsd:complexType> |
| 52 | <xsd:sequence> |
| 53 | <xsd:element ref = "CLI:CommandLine" minOccurs = "0" maxOccurs="1"/> |
| 54 | <xsd:element ref = "CLI:STDIN" minOccurs = "0" maxOccurs="1"/> |
| 55 | <xsd:element ref = "CLI:STDOUT" minOccurs = "0" maxOccurs="1"/> |
| 56 | </xsd:sequence> |
| 57 | <xsd:attribute name = "ExecutionPoint" use = "required"> |
| 58 | <xsd:annotation> |
| 59 | <xsd:documentation>Assigns a execution point for the analysis. |
| 60 | </xsd:documentation> |
| 61 | </xsd:annotation> |
| 62 | <xsd:simpleType> |
| 63 | <xsd:restriction base = "xsd:string"> |
| 64 | <xsd:enumeration value = "executeGlobal"/> |
| 65 | <xsd:enumeration value = "startDataset"/> |
| 66 | <xsd:enumeration value = "startImage"/> |
| 67 | <xsd:enumeration value = "startRegion"/> |
| 68 | <xsd:enumeration value = "finishRegion"/> |
| 69 | <xsd:enumeration value = "finishImage"/> |
| 70 | <xsd:enumeration value = "finishDataset"/> |
| 71 | </xsd:restriction> |
| 72 | </xsd:simpleType> |
| 73 | </xsd:attribute> |
| 74 | <xsd:attribute name = "MakesNewRegion" default = "false" use="optional" type = "xsd:boolean"/> |
| 75 | </xsd:complexType> |
| 76 | </xsd:element> |
| 77 | <xsd:element name = "CommandLine"> <!-- top level definition --> |
| 78 | <xsd:annotation> |
| 79 | <xsd:documentation>This describes the string that will be passed to a command line program via command line parameters. The command line handler will perform basic variable substitution on sub elements of this. |
| 80 | Example: |
| 81 | when you use the program, you type: /OME/bin/OME_Image_XYZ_stats Path=[path to repository file] Dims=[X],[Y],[Z],[W],[T],[BytesPerPix] |
| 82 | XML specification of the command line parameters is: |
| 83 | <CommandLine>Path=<RawImageFilePath/> Dims=<sizeX/>,<sizeY/>,<sizeZ/>,<sizeW/>,<sizeT/>,<BPP/></CommandLine> |
| 84 | </xsd:documentation> |
| 85 | </xsd:annotation> |
| 86 | <xsd:complexType> |
| 87 | <xsd:sequence> |
| 88 | <xsd:element ref = "CLI:Parameter" minOccurs = "0" maxOccurs = "unbounded"/> |
| 89 | </xsd:sequence> |
| 90 | </xsd:complexType> |
| 91 | <xsd:unique name = "CommandLine_XYPlaneID"> |
| 92 | <xsd:selector xpath = ".//CLI:XYPlane"/> |
| 93 | <xsd:field xpath = "@XYPlaneID"/> |
| 94 | </xsd:unique> |
| 95 | <xsd:keyref name = "CommandLine_XYPlaneID_Ref" refer = "CLI:CommandLine_XYPlaneID"> |
| 96 | <xsd:selector xpath = ".//CLI:Match"/> |
| 97 | <xsd:field xpath = "@XYPlaneID"/> |
| 98 | </xsd:keyref> |
| 99 | </xsd:element> |
| 100 | <xsd:element name = "STDIN"> <!-- top level definition --> |
| 101 | <xsd:annotation> |
| 102 | <xsd:documentation>This specifies what and how to write to STDIN. |
| 103 | Currently this is still in development. I would STRONGLY recommend contacting Josiah <siah@nih.gov> before coding against it. |
| 104 | </xsd:documentation> |
| 105 | </xsd:annotation> |
| 106 | <xsd:complexType> |
| 107 | <xsd:sequence> |
| 108 | <xsd:element ref = "CLI:InputRecord" minOccurs="1" maxOccurs = "unbounded"/> |
| 109 | </xsd:sequence> |
| 110 | </xsd:complexType> |
| 111 | </xsd:element> |
| 112 | <xsd:element name = "STDOUT"> <!-- top level definition --> |
| 113 | <xsd:annotation> |
| 114 | <xsd:documentation>This specifies what and how to read STDOUT. |
| 115 | </xsd:documentation> |
| 116 | </xsd:annotation> |
| 117 | <xsd:complexType> |
| 118 | <xsd:sequence> |
| 119 | <xsd:element ref = "CLI:OutputRecord" minOccurs="1" maxOccurs = "unbounded"/> |
| 120 | </xsd:sequence> |
| 121 | </xsd:complexType> |
| 122 | </xsd:element> |
| 123 | <xsd:element name = "Input"> <!-- top level definition --> |
| 124 | <xsd:annotation> |
| 125 | <xsd:documentation>References a particular column in a FormalInput. Used for variable substitution.</xsd:documentation> |
| 126 | </xsd:annotation> |
| 127 | <xsd:complexType> |
| 128 | <xsd:attributeGroup ref = "CLI:InputLocation"/> |
| 129 | <xsd:attribute name = "DivideBy" use="optional" type = "xsd:string"/> |
| 130 | <xsd:attribute name = "MultiplyBy" use="optional" type = "xsd:string"/> |
| 131 | </xsd:complexType> |
| 132 | </xsd:element> |
| 133 | <xsd:element name = "Output"> <!-- top level definition --> |
| 134 | <xsd:annotation> |
| 135 | <xsd:documentation>References a particular column of a FormalOutput.</xsd:documentation> |
| 136 | </xsd:annotation> |
| 137 | <xsd:complexType> |
| 138 | <xsd:sequence> |
| 139 | <xsd:element ref = "CLI:OutputTo" minOccurs="1" maxOccurs = "unbounded"/> |
| 140 | </xsd:sequence> |
| 141 | <xsd:attribute name = "AccessBy" use = "required" type = "xsd:integer"> |
| 142 | <xsd:annotation> |
| 143 | <xsd:documentation>Describes how to access information extracted using a regular expression. Examples are 1, 2, 3, ...</xsd:documentation> |
| 144 | </xsd:annotation> |
| 145 | </xsd:attribute> |
| 146 | </xsd:complexType> |
| 147 | </xsd:element> |
| 148 | <xsd:element name = "theZ"> <!-- top level definition --> |
| 149 | <xsd:annotation> |
| 150 | <xsd:documentation>Describes how the Z constraints of the XY plane should be produced or acquired.</xsd:documentation> |
| 151 | </xsd:annotation> |
| 152 | <xsd:complexType> |
| 153 | <xsd:choice minOccurs="1" maxOccurs="1"> |
| 154 | <xsd:element ref = "CLI:AutoIterate" minOccurs="1" maxOccurs="1"/> |
| 155 | <xsd:element ref = "CLI:UseValue" minOccurs="1" maxOccurs="1"/> |
| 156 | <xsd:element ref = "CLI:IterateRange" minOccurs="1" maxOccurs="1"/> |
| 157 | <xsd:element ref = "CLI:Match" minOccurs="1" maxOccurs="1"/> |
| 158 | </xsd:choice> |
| 159 | </xsd:complexType> |
| 160 | </xsd:element> |
| 161 | <xsd:element name = "theW"> <!-- top level definition --> |
| 162 | <xsd:annotation> |
| 163 | <xsd:documentation>Describes how the wavenumber constraints of the XY plane should be produced or acquired.</xsd:documentation> |
| 164 | </xsd:annotation> |
| 165 | <xsd:complexType> |
| 166 | <xsd:choice minOccurs="1" maxOccurs="1"> |
| 167 | <xsd:element ref = "CLI:AutoIterate" minOccurs="1" maxOccurs="1"/> |
| 168 | <xsd:element ref = "CLI:UseValue" minOccurs="1" maxOccurs="1"/> |
| 169 | <xsd:element ref = "CLI:IterateRange" minOccurs="1" maxOccurs="1"/> |
| 170 | <xsd:element ref = "CLI:Match" minOccurs="1" maxOccurs="1"/> |
| 171 | </xsd:choice> |
| 172 | </xsd:complexType> |
| 173 | </xsd:element> |
| 174 | <xsd:element name = "theT"> <!-- top level definition --> |
| 175 | <xsd:annotation> |
| 176 | <xsd:documentation>Describes how the time constraints of the XY plane should be produced or acquired.</xsd:documentation> |
| 177 | </xsd:annotation> |
| 178 | <xsd:complexType> |
| 179 | <xsd:choice minOccurs="1" maxOccurs="1"> |
| 180 | <xsd:element ref = "CLI:AutoIterate" minOccurs="1" maxOccurs="1"/> |
| 181 | <xsd:element ref = "CLI:UseValue" minOccurs="1" maxOccurs="1"/> |
| 182 | <xsd:element ref = "CLI:IterateRange" minOccurs="1" maxOccurs="1"/> |
| 183 | <xsd:element ref = "CLI:Match" minOccurs="1" maxOccurs="1"/> |
| 184 | </xsd:choice> |
| 185 | </xsd:complexType> |
| 186 | </xsd:element> |
| 187 | <xsd:element name = "XYPlane"> <!-- top level definition --> |
| 188 | <xsd:annotation> |
| 189 | <xsd:documentation>Describes an XY plane. Used with variable substitution. This will be substituted with a dynamically generated plane.</xsd:documentation> |
| 190 | </xsd:annotation> |
| 191 | <xsd:complexType> |
| 192 | <xsd:sequence> |
| 193 | <xsd:element ref = "CLI:theZ" minOccurs="1" maxOccurs="1"/> |
| 194 | <xsd:element ref = "CLI:theT" minOccurs="1" maxOccurs="1"/> |
| 195 | <xsd:element ref = "CLI:theW" minOccurs="1" maxOccurs="1"/> |
| 196 | </xsd:sequence> |
| 197 | <xsd:attribute name = "BPP" use="optional"> |
| 198 | <xsd:annotation> |
| 199 | <xsd:documentation>Specifies bits per pixel (BPP) the module is expecting. If the program can deal with either 8 or 16 bit images, leave this out or specify 16. Both of these result in the BPP of the image being used. That is, if the image is 8 bits, the module will get an 8 bits per pixel. If the image is 16 bits, the module will get 16 bits per pixel. |
| 200 | Currently, only native image pixels are supported. |
| 201 | </xsd:documentation> |
| 202 | </xsd:annotation> |
| 203 | <xsd:simpleType> |
| 204 | <xsd:restriction base = "xsd:integer"> |
| 205 | <xsd:enumeration value = "8"/> |
| 206 | <xsd:enumeration value = "16"/> |
| 207 | </xsd:restriction> |
| 208 | </xsd:simpleType> |
| 209 | </xsd:attribute> |
| 210 | <xsd:attribute name = "Format" use="optional"> |
| 211 | <xsd:annotation> |
| 212 | <xsd:documentation>Specifies the expected format of the plane. |
| 213 | RAW corresponds to OME repository format of pixel dump. |
| 214 | TIFF corresponds to TIFF files. |
| 215 | Currently only TIFF is supported. |
| 216 | </xsd:documentation> |
| 217 | </xsd:annotation> |
| 218 | <xsd:simpleType> |
| 219 | <xsd:restriction base = "xsd:string"> |
| 220 | <xsd:enumeration value = "RAW"/> |
| 221 | <xsd:enumeration value = "TIFF"/> |
| 222 | </xsd:restriction> |
| 223 | </xsd:simpleType> |
| 224 | </xsd:attribute> |
| 225 | <xsd:attribute name = "XYPlaneID" use="optional" type = "xsd:string"> |
| 226 | <xsd:annotation> |
| 227 | <xsd:documentation>Needed if you need another plane to match indexes. Referenced by the Match element.</xsd:documentation> |
| 228 | </xsd:annotation> |
| 229 | </xsd:attribute> |
| 230 | <xsd:attribute name = "Return" use="optional"> |
| 231 | <xsd:annotation> |
| 232 | <xsd:documentation>Specifies whether to the program needs the FilePath or the FileContents. Currently, only the FilePath is supported.</xsd:documentation> |
| 233 | </xsd:annotation> |
| 234 | <xsd:simpleType> |
| 235 | <xsd:restriction base = "xsd:string"> |
| 236 | <xsd:enumeration value = "FilePath"/> |
| 237 | <xsd:enumeration value = "File"/> |
| 238 | </xsd:restriction> |
| 239 | </xsd:simpleType> |
| 240 | </xsd:attribute> |
| 241 | <xsd:attribute name = "Pixels" use = "required" type = "xsd:string"> |
| 242 | <xsd:annotation> |
| 243 | <xsd:documentation>References a formal input of semantic type 'Pixels'</xsd:documentation> |
| 244 | </xsd:annotation> |
| 245 | </xsd:attribute> |
| 246 | </xsd:complexType> |
| 247 | </xsd:element> |
| 248 | <xsd:element name = "RawImageFilePath"> <!-- top level definition --> |
| 249 | <xsd:annotation> |
| 250 | <xsd:documentation>Used with variable substitution. This will be substituted with the path and file of the raw pixel dump image file. |
| 251 | e.g. /OME/repository/1-tinyTest.ori |
| 252 | </xsd:documentation> |
| 253 | </xsd:annotation> |
| 254 | <xsd:complexType> |
| 255 | <xsd:attribute name = "Pixels" use = "required" type = "xsd:string"> |
| 256 | <xsd:annotation> |
| 257 | <xsd:documentation>References a formal input of semantic type 'Pixels'</xsd:documentation> |
| 258 | </xsd:annotation> |
| 259 | </xsd:attribute> |
| 260 | </xsd:complexType> |
| 261 | </xsd:element> |
| 262 | <xsd:element name = "InputRecord"> <!-- top level definition --> |
| 263 | <xsd:annotation> |
| 264 | <xsd:documentation>Groups a set of inputs into records.</xsd:documentation> |
| 265 | </xsd:annotation> |
| 266 | <xsd:complexType> |
| 267 | <xsd:sequence> |
| 268 | <xsd:element ref = "CLI:Index" minOccurs="1" maxOccurs = "unbounded"/> |
| 269 | <xsd:choice minOccurs="1" maxOccurs="1"> |
| 270 | <xsd:element ref = "CLI:DelimitedRecord" minOccurs="1" maxOccurs="1"/> |
| 271 | <xsd:element ref = "CLI:CustomRecord" minOccurs="1" maxOccurs="1"/> |
| 272 | </xsd:choice> |
| 273 | </xsd:sequence> |
| 274 | </xsd:complexType> |
| 275 | <xsd:unique name = "InputRecord_XYPlaneID"> |
| 276 | <xsd:selector xpath = ".//CLI:XYPlane"/> |
| 277 | <xsd:field xpath = "@XYPlaneID"/> |
| 278 | </xsd:unique> |
| 279 | <xsd:keyref name = "InputRecord_XYPlaneID_Ref" refer = "CLI:InputRecord_XYPlaneID"> |
| 280 | <xsd:selector xpath = ".//CLI:Match"/> |
| 281 | <xsd:field xpath = "@XYPlaneID"/> |
| 282 | </xsd:keyref> |
| 283 | </xsd:element> |
| 284 | <xsd:element name = "OutputRecord"> <!-- top level definition --> |
| 285 | <xsd:annotation> |
| 286 | <xsd:documentation>Groups a set of outputs into records.</xsd:documentation> |
| 287 | </xsd:annotation> |
| 288 | <xsd:complexType> |
| 289 | <xsd:attribute name = "RepeatCount" use="optional" type = "xsd:positiveInteger"> |
| 290 | <xsd:annotation> |
| 291 | <xsd:documentation>RepeatCount specifies how many times to read a record. If it is not specified, reading will continue until it reaches the end of the output stream. |
| 292 | If used in conjunction with TerminateAt, reading will stop after RepeatCount or TerminateAt, whichever comes first. |
| 293 | </xsd:documentation> |
| 294 | </xsd:annotation> |
| 295 | </xsd:attribute> |
| 296 | <xsd:attribute name = "TerminateAt" use="optional" type = "xsd:string"> |
| 297 | <xsd:annotation> |
| 298 | <xsd:documentation>TerminateAt specifies a regular expression. When a match to this is found, reading will stop. |
| 299 | If used in conjuction with RepeatCount, reading will stop after RepeatCount or TerminateAt, whichever comes first. |
| 300 | </xsd:documentation> |
| 301 | </xsd:annotation> |
| 302 | </xsd:attribute> |
| 303 | </xsd:complexType> |
| 304 | </xsd:element> |
| 305 | <xsd:element name = "pat" type = "xsd:string"> <!-- top level definition --> |
| 306 | <xsd:annotation> |
| 307 | <xsd:documentation>Contains a regular expression. Checked for compilation when the module is imported.</xsd:documentation> |
| 308 | </xsd:annotation> |
| 309 | </xsd:element> |
| 310 | <xsd:element name = "Match"> <!-- top level definition --> |
| 311 | <xsd:annotation> |
| 312 | <xsd:documentation>Used to reference the index method used by another XYplane. Effectively syncs the planes on certain dimensions. Use with caution. Unsynced dimensions need to be compatible.</xsd:documentation> |
| 313 | </xsd:annotation> |
| 314 | <xsd:complexType> |
| 315 | <xsd:attribute name = "XYPlaneID" use = "required" type = "xsd:string"> |
| 316 | <xsd:annotation> |
| 317 | <xsd:documentation>References another Plane.</xsd:documentation> |
| 318 | </xsd:annotation> |
| 319 | </xsd:attribute> |
| 320 | </xsd:complexType> |
| 321 | </xsd:element> |
| 322 | <xsd:element name = "UseValue"> <!-- top level definition --> |
| 323 | <xsd:annotation> |
| 324 | <xsd:documentation>Use an input value. References an input, does not produce an output.</xsd:documentation> |
| 325 | </xsd:annotation> |
| 326 | <xsd:complexType> |
| 327 | <xsd:attributeGroup ref = "CLI:InputLocation"/> |
| 328 | </xsd:complexType> |
| 329 | </xsd:element> |
| 330 | <xsd:element name = "AutoIterate"> <!-- top level definition --> |
| 331 | <xsd:annotation> |
| 332 | <xsd:documentation>Iterates a dimension over its entire range. Produces outputs.</xsd:documentation> |
| 333 | </xsd:annotation> |
| 334 | <xsd:complexType> |
| 335 | <xsd:sequence> |
| 336 | <xsd:element ref = "CLI:OutputTo" minOccurs="1" maxOccurs = "unbounded"/> |
| 337 | </xsd:sequence> |
| 338 | </xsd:complexType> |
| 339 | </xsd:element> |
| 340 | <xsd:element name = "IterateRange"> <!-- top level definition --> |
| 341 | <xsd:annotation> |
| 342 | <xsd:documentation>Iterate this dimension over a range of values. Produces outputs.</xsd:documentation> |
| 343 | </xsd:annotation> |
| 344 | <xsd:complexType> |
| 345 | <xsd:sequence> |
| 346 | <xsd:element ref = "CLI:Start" minOccurs="1" maxOccurs="1"/> |
| 347 | <xsd:element ref = "CLI:End" minOccurs="1" maxOccurs="1"/> |
| 348 | <xsd:element ref = "CLI:OutputTo" minOccurs="1" maxOccurs = "unbounded"/> |
| 349 | </xsd:sequence> |
| 350 | </xsd:complexType> |
| 351 | </xsd:element> |
| 352 | <xsd:element name = "End"> <!-- top level definition --> |
| 353 | <xsd:annotation> |
| 354 | <xsd:documentation>Specifies an end point of iteration. |
| 355 | Not currently supported. |
| 356 | </xsd:documentation> |
| 357 | </xsd:annotation> |
| 358 | <xsd:complexType> |
| 359 | <xsd:attributeGroup ref = "CLI:InputLocation"/> |
| 360 | </xsd:complexType> |
| 361 | </xsd:element> |
| 362 | <xsd:element name = "Start"> <!-- top level definition --> |
| 363 | <xsd:annotation> |
| 364 | <xsd:documentation>Specifies a starting point of iteration. |
| 365 | Not currently supported. |
| 366 | </xsd:documentation> |
| 367 | </xsd:annotation> |
| 368 | <xsd:complexType> |
| 369 | <xsd:attributeGroup ref = "CLI:InputLocation"/> |
| 370 | </xsd:complexType> |
| 371 | </xsd:element> |
| 372 | <xsd:element name = "OutputTo"> <!-- top level definition --> |
| 373 | <xsd:annotation> |
| 374 | <xsd:documentation>Specifies location to write output. One data chunk that the Output element references may be written to one or more places.</xsd:documentation> |
| 375 | </xsd:annotation> |
| 376 | <xsd:complexType> |
| 377 | <xsd:attributeGroup ref = "CLI:OutputLocation"/> |
| 378 | </xsd:complexType> |
| 379 | </xsd:element> |
| 380 | <xsd:element name = "RawText" type = "xsd:string"/> <!-- top level definition --> |
| 381 | <xsd:element name = "InputSubString"> <!-- top level definition --> |
| 382 | <xsd:complexType> |
| 383 | <xsd:choice minOccurs="1" maxOccurs="1"> |
| 384 | <xsd:element ref = "CLI:Input" minOccurs="1" maxOccurs="1"/> |
| 385 | <xsd:element ref = "CLI:XYPlane" minOccurs="1" maxOccurs="1"/> |
| 386 | <xsd:element ref = "CLI:RawImageFilePath" minOccurs="1" maxOccurs="1"/> |
| 387 | <xsd:element ref = "CLI:RawText" minOccurs="1" maxOccurs="1"/> |
| 388 | </xsd:choice> |
| 389 | </xsd:complexType> |
| 390 | </xsd:element> |
| 391 | <xsd:element name = "Index"> <!-- top level definition --> |
| 392 | <xsd:annotation> |
| 393 | <xsd:documentation>This specifies what semantic elements of the attributes should be used to merge them into records. Every formalInput in a record should be included in this. |
| 394 | For records with multiple indexes, (Stack Statistics for example has theT and theC), specify two indexes. The records will be sorted based on the index order. |
| 395 | This means a stack statistics record that specifies theC as an index before theT will be sorted first on theC, then on theT. |
| 396 | </xsd:documentation> |
| 397 | </xsd:annotation> |
| 398 | <xsd:complexType> |
| 399 | <xsd:sequence> |
| 400 | <xsd:element ref = "CLI:Input" minOccurs="1" maxOccurs = "unbounded"/> |
| 401 | </xsd:sequence> |
| 402 | </xsd:complexType> |
| 403 | </xsd:element> |
| 404 | <xsd:element name = "DelimitedRecord"> <!-- top level definition --> |
| 405 | <xsd:annotation> |
| 406 | <xsd:documentation>Use this to construct a Delimited Record. (i.e. tab delimitted, comma delimitted, etc). At some point this will be expanded to include XYPlanes and RawImageFilePath.</xsd:documentation> |
| 407 | </xsd:annotation> |
| 408 | <xsd:complexType> |
| 409 | <xsd:sequence> |
| 410 | <xsd:element ref = "CLI:Input" minOccurs="1" maxOccurs = "unbounded"/> |
| 411 | </xsd:sequence> |
| 412 | <xsd:attribute name = "FieldDelimiter" use = "required" type = "xsd:string"> |
| 413 | <xsd:annotation> |
| 414 | <xsd:documentation>This string will be used to separate fields in this record.</xsd:documentation> |
| 415 | </xsd:annotation> |
| 416 | </xsd:attribute> |
| 417 | <xsd:attribute name = "RecordDelimiter" default = "\n" use="optional" type = "xsd:string"> |
| 418 | <xsd:annotation> |
| 419 | <xsd:documentation>This will be used to separate Records. Defaults to a newline (a newline as interpretted by perl).</xsd:documentation> |
| 420 | </xsd:annotation> |
| 421 | </xsd:attribute> |
| 422 | </xsd:complexType> |
| 423 | </xsd:element> |
| 424 | <xsd:element name = "CustomRecord"> <!-- top level definition --> |
| 425 | <xsd:annotation> |
| 426 | <xsd:documentation>Used to construct an arbitrarily formatted record. Not currently supported. email Josiah <siah@nih.gov> if you need this implemented.</xsd:documentation> |
| 427 | </xsd:annotation> |
| 428 | <xsd:complexType> |
| 429 | <xsd:sequence> |
| 430 | <xsd:element ref = "CLI:InputSubString" minOccurs="1" maxOccurs = "unbounded"/> |
| 431 | </xsd:sequence> |
| 432 | </xsd:complexType> |
| 433 | </xsd:element> |
| 434 | <xsd:element name = "Parameter"> <!-- top level definition --> |
| 435 | <xsd:annotation> |
| 436 | <xsd:documentation>All Formal Inputs referenced within this scope should have a count of 0 or 1.</xsd:documentation> |
| 437 | </xsd:annotation> |
| 438 | <xsd:complexType> |
| 439 | <xsd:sequence> |
| 440 | <xsd:element ref = "CLI:InputSubString" minOccurs="1" maxOccurs = "unbounded"/> |
| 441 | </xsd:sequence> |
| 442 | </xsd:complexType> |
| 443 | </xsd:element> |
| 444 | <xsd:element name = "TempFile"> <!-- top level definition --> |
| 445 | <xsd:annotation> |
| 446 | <xsd:documentation>Will be substituted with the full path of the file created. The OutputTo feature is not implemented yet.</xsd:documentation> |
| 447 | </xsd:annotation> |
| 448 | <xsd:complexType> |
| 449 | <xsd:sequence> |
| 450 | <xsd:element ref = "CLI:OutputTo" minOccurs = "0" maxOccurs = "unbounded"/> |
| 451 | </xsd:sequence> |
| 452 | <xsd:attribute name = "FileID" use="optional" type = "xsd:string"> |
| 453 | <xsd:annotation> |
| 454 | <xsd:documentation>Should uniquely identify this tempFile. It is used to retrieve the path as a variable.</xsd:documentation> |
| 455 | </xsd:annotation> |
| 456 | </xsd:attribute> |
| 457 | <xsd:attribute name = "Repository" use="optional" type = "xsd:string"> |
| 458 | <xsd:annotation> |
| 459 | <xsd:documentation>If specified, the temporary file will be located in the repository. This specifies where to find a repository attribute by FormalInputName and SemanticElementName(s). Following references is valid. e.g. Location="PixelInput.Repository"</xsd:documentation> |
| 460 | </xsd:annotation> |
| 461 | </xsd:attribute> |
| 462 | </xsd:complexType> |
| 463 | </xsd:element> |
| 464 | <xsd:element name = "PixelOutput"> <!-- top level definition --> |
| 465 | <xsd:annotation> |
| 466 | <xsd:documentation>Allows SemanticTypes Pixels and PixelsPlane to be outputs. The subelements specify locations for the population of data. |
| 467 | This data population is useful for a Plane projection algorithm that has the same X and Y dimensions as the Pixels it is operating on. |
| 468 | Alternately, these fields may be filled by ouput from STDOUT. |
| 469 | The FileSHA1 subelement is automatically calculated for the pixel dump file. |
| 470 | </xsd:documentation> |
| 471 | </xsd:annotation> |
| 472 | <xsd:complexType> |
| 473 | <xsd:sequence> |
| 474 | <xsd:element ref = "CLI:SizeX" minOccurs = "0" maxOccurs="1"/> |
| 475 | <xsd:element ref = "CLI:SizeY" minOccurs = "0" maxOccurs="1"/> |
| 476 | <xsd:element ref = "CLI:SizeZ" minOccurs = "0" maxOccurs="1"/> |
| 477 | <xsd:element ref = "CLI:SizeC" minOccurs = "0" maxOccurs="1"/> |
| 478 | <xsd:element ref = "CLI:SizeT" minOccurs = "0" maxOccurs="1"/> |
| 479 | <xsd:element ref = "CLI:PixelType" minOccurs = "0" maxOccurs="1"/> |
| 480 | <xsd:element ref = "CLI:BitsPerPixel" minOccurs = "0" maxOccurs="1"/> |
| 481 | <xsd:element ref = "CLI:Repository" minOccurs = "0" maxOccurs="1"/> |
| 482 | <xsd:element ref = "CLI:Path" minOccurs = "0" maxOccurs="1"/> |
| 483 | </xsd:sequence> |
| 484 | <xsd:attribute name = "type" use="optional"> |
| 485 | <xsd:simpleType> |
| 486 | <xsd:restriction base = "xsd:string"> |
| 487 | <xsd:enumeration value = "Pixels"/> |
| 488 | <xsd:enumeration value = "PixelsPlane"/> |
| 489 | </xsd:restriction> |
| 490 | </xsd:simpleType> |
| 491 | </xsd:attribute> |
| 492 | <xsd:attribute name = "FormalOutput" use="optional" type = "xsd:string"/> |
| 493 | <xsd:attribute name = "UseBase" use="optional" type = "xsd:string"> |
| 494 | <xsd:annotation> |
| 495 | <xsd:documentation>Unimplemented. Will subsume all subelements except <Repository> and <Path>. This will reference a formal input. That input be used for copying all possible data that has not been filled by other means. </xsd:documentation> |
| 496 | </xsd:annotation> |
| 497 | </xsd:attribute> |
| 498 | </xsd:complexType> |
| 499 | </xsd:element> |
| 500 | <xsd:element name = "SizeX"> <!-- top level definition --> |
| 501 | <xsd:annotation> |
| 502 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 503 | </xsd:annotation> |
| 504 | <xsd:complexType> |
| 505 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 506 | <xsd:annotation> |
| 507 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 508 | </xsd:annotation> |
| 509 | </xsd:attribute> |
| 510 | </xsd:complexType> |
| 511 | </xsd:element> |
| 512 | <xsd:element name = "SizeY"> <!-- top level definition --> |
| 513 | <xsd:annotation> |
| 514 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 515 | </xsd:annotation> |
| 516 | <xsd:complexType> |
| 517 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 518 | <xsd:annotation> |
| 519 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 520 | </xsd:annotation> |
| 521 | </xsd:attribute> |
| 522 | </xsd:complexType> |
| 523 | </xsd:element> |
| 524 | <xsd:element name = "SizeZ"> <!-- top level definition --> |
| 525 | <xsd:annotation> |
| 526 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 527 | </xsd:annotation> |
| 528 | <xsd:complexType> |
| 529 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 530 | <xsd:annotation> |
| 531 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 532 | </xsd:annotation> |
| 533 | </xsd:attribute> |
| 534 | </xsd:complexType> |
| 535 | </xsd:element> |
| 536 | <xsd:element name = "SizeC"> <!-- top level definition --> |
| 537 | <xsd:annotation> |
| 538 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 539 | </xsd:annotation> |
| 540 | <xsd:complexType> |
| 541 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 542 | <xsd:annotation> |
| 543 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 544 | </xsd:annotation> |
| 545 | </xsd:attribute> |
| 546 | </xsd:complexType> |
| 547 | </xsd:element> |
| 548 | <xsd:element name = "SizeT"> <!-- top level definition --> |
| 549 | <xsd:annotation> |
| 550 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 551 | </xsd:annotation> |
| 552 | <xsd:complexType> |
| 553 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 554 | <xsd:annotation> |
| 555 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 556 | </xsd:annotation> |
| 557 | </xsd:attribute> |
| 558 | </xsd:complexType> |
| 559 | </xsd:element> |
| 560 | <xsd:element name = "PixelType"> <!-- top level definition --> |
| 561 | <xsd:annotation> |
| 562 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 563 | </xsd:annotation> |
| 564 | <xsd:complexType> |
| 565 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 566 | <xsd:annotation> |
| 567 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 568 | </xsd:annotation> |
| 569 | </xsd:attribute> |
| 570 | </xsd:complexType> |
| 571 | </xsd:element> |
| 572 | <xsd:element name = "BitsPerPixel"> <!-- top level definition --> |
| 573 | <xsd:annotation> |
| 574 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 575 | </xsd:annotation> |
| 576 | <xsd:complexType> |
| 577 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 578 | <xsd:annotation> |
| 579 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 580 | </xsd:annotation> |
| 581 | </xsd:attribute> |
| 582 | </xsd:complexType> |
| 583 | </xsd:element> |
| 584 | <xsd:element name = "Repository"> <!-- top level definition --> |
| 585 | <xsd:annotation> |
| 586 | <xsd:documentation>Specifies an input data location for populating the semantic element</xsd:documentation> |
| 587 | </xsd:annotation> |
| 588 | <xsd:complexType> |
| 589 | <xsd:attribute name = "Location" use = "required" type = "xsd:string"> |
| 590 | <xsd:annotation> |
| 591 | <xsd:documentation>This specifies where to find a piece of data by FormalOutputName and SemanticElementName. i.e. To reference Semantic element 'bar' from Formal Output 'foo', Location="foo.bar"</xsd:documentation> |
| 592 | </xsd:annotation> |
| 593 | </xsd:attribute> |
| 594 | </xsd:complexType> |
| 595 | </xsd:element> |
| 596 | <xsd:element name = "Path"> <!-- top level definition --> |
| 597 | <xsd:annotation> |
| 598 | <xsd:documentation>Specifies a data location for populating the semantic element</xsd:documentation> |
| 599 | </xsd:annotation> |
| 600 | <xsd:complexType> |
| 601 | <xsd:attribute name = "FileID" use="optional" type = "xsd:string"> |
| 602 | <xsd:annotation> |
| 603 | <xsd:documentation>Refers to a TempFile</xsd:documentation> |
| 604 | </xsd:annotation> |
| 605 | </xsd:attribute> |
| 606 | </xsd:complexType> |
| 607 | </xsd:element> |
| 608 | <xsd:element name = "PixelsInput"> <!-- top level definition --> |
| 609 | <xsd:annotation> |
| 610 | <xsd:documentation>Grants file path to Pixels input. Future plans include dumping pixel file contents as well.</xsd:documentation> |
| 611 | </xsd:annotation> |
| 612 | <xsd:complexType> |
| 613 | <xsd:attributeGroup ref = "CLI:InputLocation"/> |
| 614 | <xsd:attribute name = "SubstituteWith" use = "required"> |
| 615 | <xsd:simpleType> |
| 616 | <xsd:restriction base = "xsd:string"> |
| 617 | <xsd:enumeration value = "path"/> |
| 618 | </xsd:restriction> |
| 619 | </xsd:simpleType> |
| 620 | </xsd:attribute> |
| 621 | </xsd:complexType> |
| 622 | </xsd:element> |
| 623 | </xsd:schema> |
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