From 98a53810d07341c4cd445e316c9502963d9068c9 Mon Sep 17 00:00:00 2001
From: tpietzsch <tobias.pietzsch@gmail.com>
Date: Tue, 24 Sep 2019 19:12:01 +0200
Subject: [PATCH] Change dataset pattern to "/setup%d/timepoint%d/s%d" (no
zero-padding)
---
BDV N5 format.md | 12 ++++++------
src/main/java/bdv/img/n5/BdvN5Format.java | 6 +++---
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/BDV N5 format.md b/BDV N5 format.md
index 8a98b463..0ec7a7eb 100644
--- a/BDV N5 format.md
+++ b/BDV N5 format.md
@@ -7,9 +7,9 @@ multi-resolution 3D stacks are organized in the following N5 hierarchy:
```
\
-├── setup00
+├── setup0
│ ├── attributes.json {"downsamplingFactors":[[1,1,1],[2,2,2]],"dataType":"uint8"}
-│ ├── timepoint00000
+│ ├── timepoint0
│ │ ├── s0
│ │ │ ├── attributes.json {"dataType":"uint8","compression":{"type":"bzip2","blockSize":9},"blockSize":[16,16,16],"dimensions":[400,400,25]}
│ │ │ ┊
@@ -17,14 +17,14 @@ multi-resolution 3D stacks are organized in the following N5 hierarchy:
│ │ ├── s1
│ │ ┊
│ │
-│ ├── timepoint00001
+│ ├── timepoint1
│ ┊
│
-├── setup01
+├── setup1
┊
```
-Each 3D stack is stored as a dataset with path formatted as `/setup%02d/timepoint%05d/s%d`.
+Each 3D stack is stored as a dataset with path formatted as `/setup%d/timepoint%d/s%d`.
Here, `setup` number is flattened index of channel, angle, tile, illumination, etc.,
`timepoint` is the index of the time point, and `s` is the scale level of the multi-resolution pyramid.
@@ -38,7 +38,7 @@ that specify downsampling scheme and datatype, which are the same for all timepo
`downsamplingFactors` specifies power-of-two downscaling factors for each scale level (with respect to full resolution `s0`, which always has `[1,1,1]`).
`dataType` is one of {uint8, uint16, uint32, uint64, int8, int16, int32, int64, float32, float64}.
-> TODO: Additional metadata (for example identifying `setup03` as channel 3, tile 124, etc.) could be replicated from the XML.
+> TODO: Additional metadata (for example identifying `setup3` as channel 3, tile 124, etc.) could be replicated from the XML.
The idea would be that parts of a dataset can be used independent of BDV, without the XML.
We should agree on standard attributes for this.
diff --git a/src/main/java/bdv/img/n5/BdvN5Format.java b/src/main/java/bdv/img/n5/BdvN5Format.java
index f4d4d69b..fb2dfb4e 100644
--- a/src/main/java/bdv/img/n5/BdvN5Format.java
+++ b/src/main/java/bdv/img/n5/BdvN5Format.java
@@ -7,16 +7,16 @@ public class BdvN5Format
public static String getPathName( final int setupId )
{
- return String.format( "setup%02d", setupId );
+ return String.format( "setup%d", setupId );
}
public static String getPathName( final int setupId, final int timepointId )
{
- return String.format( "setup%02d/timepoint%05d", setupId, timepointId );
+ return String.format( "setup%d/timepoint%d", setupId, timepointId );
}
public static String getPathName( final int setupId, final int timepointId, final int level )
{
- return String.format( "setup%02d/timepoint%05d/s%d", setupId, timepointId, level );
+ return String.format( "setup%d/timepoint%d/s%d", setupId, timepointId, level );
}
}
--
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