Updated README, added example reg instructions.

README.md

@@ -2,20 +2,20 @@
 Tensor Image Registration Library
 
 
-If you are installing TIRL from source, you may create a separate 
-enviroment for your installation using the provided tirlenv.yml environment 
-descriptor file. 
+If you are installing TIRL from source, you may create a separate
+enviroment for your installation using the provided tirlenv.yml environment
+descriptor file.
 
 ## FSL Installation
 
-TIRL may be already installed on your system as part of FSL. To use this 
+TIRL may be already installed on your system as part of FSL. To use this
 installation, activate the ```fslpython``` conda environment:
 
 ```shell script
 source $FSLDIR/fslpython/bin/activate fslpython
 ```
 
-The TIRL executable should now be accessible by typing ```tirl``` in your 
+The TIRL executable should now be accessible by typing ```tirl``` in your
 terminal:
 
 ```shell script
@@ -24,9 +24,9 @@ tirl
 
 ## Installation from source
 
-If you would like to use a more recent version of TIRL than what is installed 
-with FSL, you can install the library from source. It is recommended that you 
-create a separate conda environment for this purpose, as outlined below. 
+If you would like to use a more recent version of TIRL than what is installed
+with FSL, you can install the library from source. It is recommended that you
+create a separate conda environment for this purpose, as outlined below.
 
 1. Download the TIRL source code.
 
@@ -53,32 +53,39 @@ conda activate tirlenv
 
 ```shell script
 python setup.py install
+```
+
+5. On some machines, the installer may not find the openBLAS headers in the conda environment automatically, and the installer will raise an error that "lapacke.h" was not found. If this happens to you, configure this environment variable, that will allow the gcc compiler to find the required header files. Type the following in your terminal while you are within tirlenv. You must deactivate and reactivate the environment after this step.
 
+```shell script
+conda env config vars set C_INCLUDE_PATH=${CONDA_PREFIX}/include:${C_INCLUDE_PATH}
 ```
 
+If the variable is set, follow step 4 to install TIRL.
+
 ## Configuration
 
-Note: to configure TIRL, you must be within the Python environment where you 
+Note: to configure TIRL, you must be within the Python environment where you
 installed TIRL ('tirlenv' in the above example).
 
-To configure TIRL for your system, type ```tirl config``` in your terminal 
+To configure TIRL for your system, type ```tirl config``` in your terminal
 window. This will allow you to edit the configuration parameters using vim.
 
 To use another editor, e.g. nano, type ```tirl config nano```. Other options
-might include subl (Sublime Text), atom (Atom), or emacs (Emacs), depending on 
+might include subl (Sublime Text), atom (Atom), or emacs (Emacs), depending on
 what is available on your system.
 
-Before you start using TIRL, you must make sure that the **temporary working 
-directory (TWD)** is set correctly. You should have write access to this 
-folder, and ideally it should be on a fast-access storage device such as an 
-NVME SSD. TIRL will use this folder to deposit large files to avoid overloading 
-the system memory. Files will normally disappear from this folder after a tirl 
-script finishes, but if you notice that the files in this folder occupy a lot 
+Before you start using TIRL, you must make sure that the **temporary working
+directory (TWD)** is set correctly. You should have write access to this
+folder, and ideally it should be on a fast-access storage device such as an
+NVME SSD. TIRL will use this folder to deposit large files to avoid overloading
+the system memory. Files will normally disappear from this folder after a tirl
+script finishes, but if you notice that the files in this folder occupy a lot
 of disk space, you should delete them manually.
 
 ## Basic test
 
-1. Open the python shell by typing ```python``` in the terminal window (make 
+1. Open the python shell by typing ```python``` in the terminal window (make
 sure that you have previously activated the 'tirlenv' environment).
 
 2. Type the following in the interactive shell:
@@ -91,7 +98,8 @@ img.preview()
 
 ### Full test ###
 
-1. Make sure that the *coverage* library is installed in your environment:
+1. Unless you used the tirlenv.yml file to create your environment, you should
+first make sure that the *coverage* library is installed in your environment:
 
 ```shell script
 conda install coverage
@@ -103,5 +111,11 @@ conda install coverage
 python test.py
 ```
 
-If all tests are successful, a line-by-line coverage report will be generated 
-in HTML format that you can view in your browser.
\ No newline at end of file
+If all tests are successful, a line-by-line coverage report will be generated
+in HTML format that you can view in your browser.
+
+3. To test a single module of TIRL (e.g. chain.py), run:
+
+```shell script
+python test.py test_chain
+```

share/example/example_reg_commands.sh

+#!/bin/sh
+
+# Runs the example registration pipeline
+
+EXAMPLE="."
+tirl histology_to_block --config ${EXAMPLE}/config/1_histology_to_block.json --verbose
+tirl find_sites ${EXAMPLE}/3_brain_slice/*.tif --verbose
+tirl block_to_slice --config ${EXAMPLE}/config/2_block_to_slice.json --verbose
+tirl slice_to_volume --config ${EXAMPLE}/config/3_slice_to_volume.json --verbose
+tirl combine --histo ${EXAMPLE}/stage1/fixed4_nonlinear.timg --block ${EXAMPLE}/stage2/fixed4_nonlinear.timg --slice ${EXAMPLE}/stage3/4_stage4.timg --vol ${EXAMPLE}/stage3/volume.timg --out ${EXAMPLE}/combined