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ImageJ plugin - Group files Exception #1967

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merged 5 commits into from
Sep 30, 2015
Merged

ImageJ plugin - Group files Exception #1967

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537752e
ImageJ plugin - Exception when both 'group files' and 'open individua…
dgault Sep 7, 2015
605c056
Update to only show the warning dialog when user has selected group f…
dgault Sep 10, 2015
6f8847a
Updating text to be displayed
dgault Sep 16, 2015
fc0d1a2
Spelling and formatting updates
dgault Sep 25, 2015
38d572d
Text Update
dgault Sep 30, 2015
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6 changes: 4 additions & 2 deletions components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java
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Original file line number Diff line number Diff line change
Expand Up @@ -492,7 +492,7 @@ private void initializeFile() throws FormatException, IOException {

BF.status(options.isQuiet(), "Analyzing " + getIdName());
baseReader.setMetadataFiltered(true);
baseReader.setGroupFiles(!options.isUngroupFiles());
baseReader.setGroupFiles(!options.isUngroupFiles() || options.isGroupFiles());
if(options != null && !options.showROIs()){
MetadataOptions mo = baseReader.getMetadataOptions();
if(mo == null){
Expand All @@ -504,6 +504,8 @@ private void initializeFile() throws FormatException, IOException {
}
baseReader.setId(options.getId());

boolean mustGroup = baseReader.fileGroupOption(options.getId()) == FormatTools.MUST_GROUP;
options.setMustGroup(mustGroup);
}

/** Performed following ImportStep.STACK notification. */
Expand All @@ -515,7 +517,7 @@ private void initializeStack() throws FormatException, IOException {

// overwrite base filename with file pattern
String id = options.getId();
options.setId(id);
fileStitcher.setId(id);
fileStitcher.setUsingPatternIds(true);
fileStitcher.setCanChangePattern(false);
}
Expand Down
8 changes: 7 additions & 1 deletion components/bio-formats-plugins/src/loci/plugins/in/ImporterOptions.java
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Expand Up @@ -77,7 +77,8 @@ public class ImporterOptions extends OptionsList {
public static final String KEY_VIRTUAL = "virtual";
public static final String KEY_WINDOWLESS = "windowless";
public static final String KEY_STITCH_TILES = "stitchTiles";

public static final String KEY_MUST_GROUP = "mustGroup";

// possible values for colorMode
public static final String COLOR_MODE_DEFAULT = "Default";
public static final String COLOR_MODE_COMPOSITE = "Composite";
Expand Down Expand Up @@ -396,6 +397,11 @@ public boolean isViewView5D() {
public boolean doStitchTiles() { return isSet(KEY_STITCH_TILES); }
public void setStitchTiles(boolean b) { setValue(KEY_STITCH_TILES, b); }

// mustGroup
public String getMustGroupInfo() { return getInfo(KEY_MUST_GROUP); }
public boolean doMustGroup() { return isSet(KEY_MUST_GROUP); }
public void setMustGroup(boolean b) { setValue(KEY_MUST_GROUP, b); }

// -- ImporterOptions methods - secondary options accessors and mutators --

// series options
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9 changes: 8 additions & 1 deletion components/bio-formats-plugins/src/loci/plugins/in/ImporterPrompter.java
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Expand Up @@ -27,6 +27,7 @@

package loci.plugins.in;

import ij.IJ;
import loci.common.StatusEvent;
import loci.common.StatusListener;
import loci.plugins.BF;
Expand Down Expand Up @@ -78,7 +79,13 @@ public void statusUpdated(StatusEvent e) {
if (!promptMain()) process.cancel();
break;
case STACK:
if (!promptFilePattern()) process.cancel();
ImporterOptions options = process.getOptions();
if (options != null && options.doMustGroup() && options.isGroupFiles()) {
IJ.showMessage("Bio-Formats",
"File Stitching Options are not available for files of this format.\n"
+ "Files will be grouped according to image format specifications.\n");
}
else if (!promptFilePattern()) process.cancel();
break;
case SERIES:
if (!promptSeries()) process.cancel();
Expand Down
5 changes: 5 additions & 0 deletions components/bio-formats-plugins/src/loci/plugins/in/importer-options.txt
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Expand Up @@ -339,3 +339,8 @@ default = false
type = boolean
label = windowless
default = false

[mustGroup]
type = boolean
label = mustGroup
default = false