[ome-users] issue and fix for MetaXpress multi-line descriptions

[Mario Emmenlauer]

Dear Bio-Formats developers,

I have a small issue with MetaXpress meta data, and a possible fix.
When I read the image (link below), there are several global metadata
entries that are not correct. I followed up where they come from, and
it turns out that MetaXpress has a free-text box where user can enter
a 'Description' for their screening experiment. Multi-line entry is
supported in MetaXpress, which leads to "wrong" interpretation of the
metadata in Bio-Formats.

Here the example from the image below. For the field 'Description'
our user had entered in MetaXpress:
    siRNA transfection of HeLa cells
    Entry 4h
    extracellular: red
    intracellular: red and green
    DAPI staining (1:1000)
    [...]

Of this Description, several lines are missing in Bio-Formats. For
the text that is not missing, I can find fields like:
    'extracellular'          'red'
    'intracellular'          'red and green'
    'DAPI staining (1'       '1000)'

This is not how I think the metadata should be reported :-)


The best solution I could think of is a defined vocabulary of keys
from MetaXpress, to separate them from the free-text entered by the
user. Attached is a patch that does exactly this, and works well
for me. The patch should apply smoothly to Bio-Formats 5.0.7 file
components/formats-gpl/src/loci/formats/in/MetamorphReader.java

For me, the patch achieves a second functionality: there are some
keys that do not have a colon, in other words they consist only of
a key and no value (an example is "Acquired from Photometrics"). For
me it makes sense to store them as both key and value, i.e. to have
it reported as:
    'Acquired from Photometrics' = 'Acquired from Photometrics'

This is my personal preference, you can ignore this part of the patch
if you do not find it useful.

One last thing: I store the free-text in key 'Global Description'.
I think for you its more common to use the key 'Global Comment'? Feel
free to change this to your liking.


The image I used is here:
    http://data.marssoft.de/bBZIX-021_wD13_s3_z0_t1_cCy5_u001.tif

All the best, and thanks for your great work,

     Mario Emmenlauer






-- 
Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
D-81669 München                          http://www.marioemmenlauer.de/

-------------- next part --------------
diff --git a/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java b/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java
index c414150..57efb81 100644
--- a/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java
+++ b/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java
@@ -64,6 +64,15 @@ public class MetamorphHandler extends BaseHandler {
   private String stageLabel;
   private Double gain;
 
+  private String[] mDesciptionKeyList = {
+    "Plate Screen", "Acquired from Photometrics", "Barcode:",
+    "Experiment base name:", "Experiment set:", "Exposure:",
+    "Binning:", "Region:", "Subtract:", "Shading:", "Digitizer:",
+    "Gain:", "Camera Shutter:", "Clear Count:", "Clear Mode:",
+    "Frames to Average:", "Trigger Mode:", "Temperature:"
+  };
+
+
   // -- Constructor --
 
   public MetamorphHandler() {
@@ -130,6 +139,8 @@ public class MetamorphHandler extends BaseHandler {
         String k = null, v = null;
 
         if (value.indexOf(delim) != -1) {
+          String vDescription = null;
+
           int currentIndex = -delim.length();
           while (currentIndex != -1) {
             currentIndex += delim.length();
@@ -144,14 +155,46 @@ public class MetamorphHandler extends BaseHandler {
             }
             currentIndex = nextIndex;
 
-            int colon = line.indexOf(":");
-            if (colon != -1) {
-              k = line.substring(0, colon).trim();
-              v = line.substring(colon + 1).trim();
-              if (metadata != null) metadata.put(k, v);
-              checkKey(k, v);
+            if (line.isEmpty()) {
+              continue;
+            }
+
+            // We use a dictionary to identify the standard MetaMorph keys:
+            boolean vLineIsMetaMorphStandard = false;
+            for (String vDescriptionKey : mDesciptionKeyList) {
+              if (line.startsWith(vDescriptionKey)) {
+                vLineIsMetaMorphStandard = true;
+                break;
+              }
+            }
+            if (vLineIsMetaMorphStandard) {
+              // The majority of tags can be split at the colon:
+              int colon = line.indexOf(":");
+              if (colon != -1) {
+                k = line.substring(0, colon).trim();
+                v = line.substring(colon + 1).trim();
+                if (metadata != null) metadata.put(k, v);
+                checkKey(k, v);
+              } else {
+                // There was no colon, so the key is a full line:
+                k = line.trim();
+                v = line.trim();
+                if (metadata != null) metadata.put(k, v);
+                checkKey(k, v);
+              }
+            } else {
+              // This is NOT a standard tag in the description field, so it
+	      // must be a multi-line description from the user (i.e. from
+	      // the MetaXpress free-text "Description" field in the screening
+	      // application).
+              if (vDescription == null) {
+                vDescription = line;
+              } else {
+                vDescription = vDescription + "\n" + line;
+              }
             }
           }
+          if (metadata != null && vDescription != null) metadata.put("Description", vDescription);
         }
         else {
           int colon = value.indexOf(":");