Changeset 4768


Ignore:
Timestamp:
02/02/09 09:12:08 (11 years ago)
Author:
melissa
Message:

Updated metadata support documentation for MetamorphReader. Also added a target to the bio-formats-auto build file that will regenerate the metadata support documentation.

Location:
trunk/components
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/components/bio-formats-auto/build.properties

    r4612 r4768  
    1919component.main-class     = MetadataAutogen 
    2020component.runtime-cp     = ${component.classpath} 
     21component.meta-support-class = MetaSupportAutogen 
  • trunk/components/bio-formats-auto/build.xml

    r4612 r4768  
    2222  </target> 
    2323 
     24  <target name="gen-meta-support" depends="compile" 
     25    description="generate documentation for Bio-Formats' metadata support"> 
     26    <java classname="${component.meta-support-class}" 
     27      classpath="${classes.dir}:${component.runtime-cp}" 
     28      fork="true" dir="${root.dir}/components/bio-formats/"> 
     29        <arg value="${omexml.version}"/> 
     30    </java> 
     31  </target> 
     32 
    2433  <target name="gen-ice" depends="compile" 
    2534    description="generate code for Bio-Formats Ice framework"> 
  • trunk/components/bio-formats-auto/src/meta-support.txt

    r4747 r4768  
    430430Dimensions.PhysicalSizeX = Yes 
    431431Dimensions.PhysicalSizeY = Yes 
    432 LogicalChannel.SamplesPerPixel = Yes 
     432Dimensions.PhysicalSizeZ = Yes 
     433LogicalChannel.SamplesPerPixel = Yes 
     434LogicalChannel.Name = Yes 
    433435Plane = Yes 
    434436PlaneTiming = Yes 
     
    436438Image.Description = Yes 
    437439ImagingEnvironment.Temperature = Yes 
     440StagePosition.PositionX = Yes 
     441StagePosition.PositionY = Yes 
     442ImagingEnvironment.Temperature = Yes 
     443DetectorSettings.Binning = Yes 
     444DetectorSettings.ReadOutRate = Yes 
     445DetectorSettings.Detector = Yes 
     446LightSourceSettings.LightSource = Yes 
     447LightSourceSettings.Wavelength = Yes 
     448Detector.Zoom = Yes 
     449Detector.Type = Missing 
    438450 
    439451[MetamorphTiffReader] 
  • trunk/components/bio-formats/doc/meta-summary.html

    r4764 r4768  
    280280    <tr> 
    281281      <td><a href="https://skyking.microscopy.wisc.edu/trac/java/wiki/MetamorphReader">MetamorphReader</a></td> 
    282       <td>28</td> 
    283       <td>0</td> 
    284       <td>0</td> 
    285       <td>285</td> 
     282      <td>38</td> 
     283      <td>0</td> 
     284      <td>0</td> 
     285      <td>275</td> 
    286286    </tr> 
    287287    <tr> 
     
    681681    <tr> 
    682682      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Detector">Detector</a>: Zoom</td> 
    683       <td>2</td> 
    684       <td>0</td> 
    685       <td>0</td> 
    686       <td>61</td> 
     683      <td>3</td> 
     684      <td>0</td> 
     685      <td>0</td> 
     686      <td>60</td> 
    687687    </tr> 
    688688    <tr> 
    689689      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef">DetectorSettings</a>: Binning</td> 
    690       <td>4</td> 
    691       <td>2</td> 
    692       <td>0</td> 
    693       <td>57</td> 
     690      <td>5</td> 
     691      <td>2</td> 
     692      <td>0</td> 
     693      <td>56</td> 
    694694    </tr> 
    695695    <tr> 
    696696      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef">DetectorSettings</a>: Detector</td> 
    697       <td>2</td> 
    698       <td>2</td> 
    699       <td>0</td> 
    700       <td>59</td> 
     697      <td>3</td> 
     698      <td>2</td> 
     699      <td>0</td> 
     700      <td>58</td> 
    701701    </tr> 
    702702    <tr> 
     
    716716    <tr> 
    717717      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef">DetectorSettings</a>: ReadOutRate</td> 
    718       <td>3</td> 
    719       <td>2</td> 
    720       <td>0</td> 
    721       <td>58</td> 
     718      <td>4</td> 
     719      <td>2</td> 
     720      <td>0</td> 
     721      <td>57</td> 
    722722    </tr> 
    723723    <tr> 
     
    765765    <tr> 
    766766      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels">Dimensions</a>: PhysicalSizeZ</td> 
    767       <td>21</td> 
    768       <td>0</td> 
    769       <td>0</td> 
    770       <td>42</td> 
     767      <td>22</td> 
     768      <td>0</td> 
     769      <td>0</td> 
     770      <td>41</td> 
    771771    </tr> 
    772772    <tr> 
     
    13811381    <tr> 
    13821382      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef">LightSourceSettings</a>: LightSource</td> 
    1383       <td>2</td> 
    1384       <td>0</td> 
    1385       <td>0</td> 
    1386       <td>61</td> 
     1383      <td>3</td> 
     1384      <td>0</td> 
     1385      <td>0</td> 
     1386      <td>60</td> 
    13871387    </tr> 
    13881388    <tr> 
    13891389      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef">LightSourceSettings</a>: Wavelength</td> 
    1390       <td>4</td> 
    1391       <td>0</td> 
    1392       <td>0</td> 
    1393       <td>59</td> 
     1390      <td>5</td> 
     1391      <td>0</td> 
     1392      <td>0</td> 
     1393      <td>58</td> 
    13941394    </tr> 
    13951395    <tr> 
     
    15071507    <tr> 
    15081508      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel">LogicalChannel</a>: Name</td> 
    1509       <td>14</td> 
    1510       <td>3</td> 
    1511       <td>0</td> 
    1512       <td>46</td> 
     1509      <td>15</td> 
     1510      <td>3</td> 
     1511      <td>0</td> 
     1512      <td>45</td> 
    15131513    </tr> 
    15141514    <tr> 
     
    24662466    <tr> 
    24672467      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition">StagePosition</a>: PositionX</td> 
    2468       <td>10</td> 
    2469       <td>0</td> 
    2470       <td>0</td> 
    2471       <td>53</td> 
     2468      <td>11</td> 
     2469      <td>0</td> 
     2470      <td>0</td> 
     2471      <td>52</td> 
    24722472    </tr> 
    24732473    <tr> 
    24742474      <td><a href="http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition">StagePosition</a>: PositionY</td> 
    2475       <td>10</td> 
    2476       <td>0</td> 
    2477       <td>0</td> 
    2478       <td>53</td> 
     2475      <td>11</td> 
     2476      <td>0</td> 
     2477      <td>0</td> 
     2478      <td>52</td> 
    24792479    </tr> 
    24802480    <tr> 
  • trunk/components/bio-formats/doc/meta/MetamorphReader.txt

    r4764 r4768  
    1010 
    1111Of the 313 fields documented below: 
    12   * The file format itself supports 28 of them (8%). 
    13   * Of those, Bio-Formats fully or partially converts 28 (100%). 
     12  * The file format itself supports 38 of them (12%). 
     13  * Of those, Bio-Formats fully or partially converts 38 (100%). 
    1414 
    1515== Supported fields == 
    1616These fields are fully supported by the 
    1717Bio-Formats Metamorph STK format reader: 
     18  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Detector Detector]: Zoom 
     19  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Binning 
     20  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Detector 
     21  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: ReadOutRate 
    1822  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Dimensions]: PhysicalSizeX 
    1923  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Dimensions]: PhysicalSizeY 
     24  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Dimensions]: PhysicalSizeZ 
    2025  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Experimenter Experimenter]: Email 
    2126  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Experimenter Experimenter]: FirstName 
     
    2732  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Image Image]: Description 
    2833  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_ImagingEnvironment ImagingEnvironment]: Temperature 
     34  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef LightSourceSettings]: LightSource 
     35  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef LightSourceSettings]: Wavelength 
     36  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: Name 
    2937  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: SamplesPerPixel 
    3038  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Pixels]: BigEndian - since r639 
     
    4452  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_PlaneTiming PlaneTiming]: DeltaT 
    4553  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_PlaneTiming PlaneTiming]: ExposureTime 
    46 === Total supported: 28 === 
     54  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition StagePosition]: PositionX 
     55  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition StagePosition]: PositionY 
     56=== Total supported: 38 === 
    4757 
    4858== Unknown or missing fields == 
     
    7686  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Detector Detector]: Type 
    7787  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Detector Detector]: Voltage 
    78   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Detector Detector]: Zoom 
    79   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Binning 
    80   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Detector 
    8188  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Gain 
    8289  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Offset 
    83   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: ReadOutRate 
    8490  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_DetectorRef DetectorSettings]: Voltage 
    8591  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Dichroic Dichroic]: LotNumber 
    8692  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Dichroic Dichroic]: Manufacturer 
    8793  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Dichroic Dichroic]: Model 
    88   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Dimensions]: PhysicalSizeZ 
    8994  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Dimensions]: TimeIncrement 
    9095  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Pixels Dimensions]: WaveIncrement 
     
    165170  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef LightSourceRef]: Wavelength 
    166171  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef LightSourceSettings]: Attenuation 
    167   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef LightSourceSettings]: LightSource 
    168   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LightSourceRef LightSourceSettings]: Wavelength 
    169172  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Line Line]: ID 
    170173  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Line Line]: transform 
     
    183186  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: LightSource 
    184187  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: Mode 
    185   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: Name 
    186188  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: NdFilter 
    187189  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_LogicalChannel LogicalChannel]: OTF 
     
    303305  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StageLabel StageLabel]: Y 
    304306  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StageLabel StageLabel]: Z 
    305   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition StagePosition]: PositionX 
    306   * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition StagePosition]: PositionY 
    307307  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_StagePosition StagePosition]: PositionZ 
    308308  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_Thumbnail Thumbnail]: ID 
     
    335335  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_WellSample WellSample]: Timepoint 
    336336  * [http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_WellSampleRef WellSampleRef]: ID 
    337 === Total unknown or missing: 285 === 
     337=== Total unknown or missing: 275 === 
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