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Add support of Plate Info Metadata in Bio-Formats reader
- Removes unnecessary reader argument in BioFormatsHelper - Removes model reader which was created for each opener: this had a huge performance impact - The model is memoized - If the bioformats reader is associated to a plate, the plate info is added as entities (Plate, Well, Field (= WellSample)) - Adds the required entities and serializers
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| /*- | ||
| * #%L | ||
| * Various image loaders for bigdataviewer (Bio-Formats, Omero, QuPath) | ||
| * %% | ||
| * Copyright (C) 2022 - 2024 ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP) | ||
| * %% | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public | ||
| * License along with this program. If not, see | ||
| * <http://www.gnu.org/licenses/gpl-3.0.html>. | ||
| * #L% | ||
| */ | ||
|
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| package ch.epfl.biop.bdv.img.entity; | ||
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| import mpicbg.spim.data.generic.base.Entity; | ||
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| public class Field extends Entity implements | ||
| Comparable<Field> | ||
| { | ||
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| public Field(final int id) { | ||
| super(id); | ||
| } | ||
|
|
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| /** | ||
| * Compares the {@link #getId() ids}. | ||
| */ | ||
| @Override | ||
| public int compareTo(final Field o) { | ||
| return getId() - o.getId(); | ||
| } | ||
|
|
||
| /** | ||
| * Empty constructor strictly necessary for dataset deserialization | ||
| */ | ||
| protected Field() {} | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| /*- | ||
| * #%L | ||
| * Various image loaders for bigdataviewer (Bio-Formats, Omero, QuPath) | ||
| * %% | ||
| * Copyright (C) 2022 - 2024 ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, BioImaging And Optics Platform (BIOP) | ||
| * %% | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License, or (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public | ||
| * License along with this program. If not, see | ||
| * <http://www.gnu.org/licenses/gpl-3.0.html>. | ||
| * #L% | ||
| */ | ||
|
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| package ch.epfl.biop.bdv.img.entity; | ||
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| import mpicbg.spim.data.generic.base.NamedEntity; | ||
|
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| public class Plate extends NamedEntity implements | ||
| Comparable<Plate> | ||
| { | ||
|
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| public Plate(final int id, final String name) { | ||
| super(id, name); | ||
| } | ||
|
|
||
| /** | ||
| * Compares the {@link #getId() ids}. | ||
| */ | ||
| @Override | ||
| public int compareTo(final Plate o) { | ||
| return getId() - o.getId(); | ||
| } | ||
|
|
||
| /** | ||
| * Empty constructor strictly necessary for dataset deserialization | ||
| */ | ||
| protected Plate() {} | ||
| } |
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