Merge pull request #14 from magnostherobot/trh/utility-scripts

Move to supporting `czinspect` in utility scripts

Makefile

@@ -18,5 +18,5 @@ test:
 	$(MAKE) test -C src/czinspect
 
 bin: all
-	ln -s ./src/regions/get_region  ./bin/get_region
-	ln -s ./src/czinspect/czinspect ./bin/czinspect
+	ln -fs ../src/regions/get_region  ./bin/get_region
+	ln -fs ../src/czinspect/czinspect ./bin/czinspect

README.md

@@ -1,4 +1,4 @@
-# CZI Extractor ![Build Status](https://travis-ci.com/magnostherobot/zeiss.svg?branch=master)
+# CZI Extractor [![Build Status](https://travis-ci.com/magnostherobot/zeiss.svg?token=w7ew2jpnKbReLg9cZxN1&branch=master)](https://travis-ci.com/magnostherobot/zeiss)
 
 Software for extracting images and metadata from Carl Zeiss Images (`.czi`
 files). This format is in use in microscopy.
@@ -8,10 +8,12 @@ data from already-existing `.czi`s.
 
 ## Requirements
 
+### `vips`
+
 These tools require [vips](https://github.com/jcupitt/libvips) version 8 or
-greater, and uuid development tools.
+greater.
 
-### Ubuntu
+#### Ubuntu
 
 Xenial Ubuntu and onward can install vips using `apt-get`:
 ```bash
@@ -20,42 +22,54 @@ sudo apt-get install libvips-dev
 Older versions may be able to
 [build from source](https://github.com/jcupitt/libvips/wiki/Build-for-Ubuntu#building-from-source).
 
-Either way, uuid development headers are also required:
-```bash
-sudo apt-get install uuid-dev
-```
-
-### OSX
+#### MacOS
 
-Mac users can install dependencies via [`brew`](https://brew.sh/):
+Mac users can install `vips` via [`brew`](https://brew.sh/):
 ```bash
 brew install vips --with-imagemagick --without-graphicsmagick --with-openexr --with-openslide
-brew install ossp-uuid
 ```
 
-### Fedora
+#### Fedora
 ```bash
-sudo dnf install vips vips-devel uuid-devel
+sudo dnf install vips vips-devel
 ```
 
-### Debian
+#### Debian
 ```bash
-sudo apt-get install libvips-dev uuid-dev
+sudo apt-get install libvips-dev
 ```
 
+### `libuuid` Development Headers
+
+The `libuuid` development headers are also required for building.
+These can usually be installed using your system package manager, or can be
+[built from source](https://github.com/karelzak/util-linux/tree/master/libuuid).
+
+### `JxrDecApp`
+
+Microsoft's JPEG-XR decoding tool `JxrDecApp` is required on the system's
+`PATH`. Some operating systems may have a package for this, or it can be
+[built from source](https://github.com/curasystems/jxrlib/blob/master/Makefile)
+(only `JxrDecApp` is required from this codebase, so all necessary building can
+be done using `make JxrDecApp`).
+
 ## Building
 
 Building should be as simple as
 ```bash
 make
 ```
-**Note**: due to a conflict in different `ld` implementations, OSX cannot build
-this project right now.
+**Note**: due to a conflict in different `ld` implementations, MacOS cannot
+build this project right now.
 
 Tests are also available:
 ```bash
 make test
 ```
+To move all of the built binaries to the `bin` folder:
+```bash
+make bin
+```
 
 ## Running
 
@@ -66,20 +80,18 @@ Each of the utility programs can be found in the appropriate `src` subfolder.
 Documentation for the use of these utilities is currently non-existant. All
 utilities have help-text that should be kept up-to-date:
 ```bash
-./src/extractjxr/extractjxr --help
-./src/regions/get_region --help
-./src/czinspect/czinspect --help
+get_region -h
+czinspect  -h
 ```
 
 ### Scripts
 
 Some utility scripts have been supplied in the `bin` folder:
 
-- `deczi.sh` is the main script for handling the extraction and conversion of
-`.czi` files.
 - `batch.sh` is a script designed to batch-process a bunch of `.czi` files at
 once.
-- `czi2png.sh` and `jxr2png.sh` are old scripts no longer used.
+- `czi2png.sh`, `jxr2png.sh`, and `deczi-extracjxr.sh`
+are old scripts no longer used.
 
 ### Example Use
 
@@ -90,7 +102,7 @@ and you want to extract every image tile (converted to `.png`s)
 from each of these files into respective subdirectories under the directory
 `extracted-tiles`:
 ```bash
-batch.sh -pd "extracted-tiles" "czi-folder"
+batch.sh -Ed "extracted-tiles" "czi-folder"
 ```
 Each set of `.png`s will turn up in a subdirectory of `extracted-tiles` named
 after the `.czi` file they came from.
@@ -102,7 +114,7 @@ residing in the directory `all-extracted`, and now you want a `123x789`-sized
 region with its top-left corner at x-y coordinate `3030,2929` of the whole
 image. Additionally, you want the output to be a `.png`
 called `my-region.png`, and the output image
-to be a zoom level 8. The appropriate command would be:
+to be at zoom level 8. The appropriate command would be:
 ```bash
 get_region -i "all-extracted" -l 3030 -u 2929 -r 3153 -d 3718 -o "my-region.png" -z 8
 ```

bin/batch.sh

@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -x
 
 set -e
 
@@ -26,7 +26,7 @@ error () {
 outdir=""
 opts=""
 
-while getopts "Ehd:aes:" opt; do
+while getopts "EShd:f:gaes:" opt; do
     case $opt in
     d)
         outdir="$OPTARG"
@@ -35,10 +35,10 @@ while getopts "Ehd:aes:" opt; do
         usage
         exit 0
         ;;
-    E|a|e)
+    E|S|a|e|g)
         opts="$opts -$opt"
         ;;
-    s)
+    s|f)
         opts="$opts -$opt $OPTARG"
         ;;
     esac