Merge pull request #22 from notZaki/Switch2Dict

Get dcm_write() to work. Switch to using Dict for handling data.

.gitignore

@@ -0,0 +1,2 @@
+# Ignore test data
+test/testdata/*

.travis.yml

@@ -4,5 +4,8 @@ os:
  - osx
 julia:
  - 0.6
+ - nightly
 notifications:
  email: false
+after_success:
+ - julia -e 'cd(Pkg.dir("DICOM")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2012-2013: Jeff Bezanson and contributors.
+Copyright (c) 2012-2018: Jeff Bezanson and contributors.
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

README.md

@@ -1 +1,73 @@
-DICOM interface for the Julia language.
+# DICOM.jl
+
+Julia interface for parsing/writing DICOM files
+
+## Usage
+
+**Installation** 
+
+To install the package:
+```
+julia> Pkg.add("DICOM")
+```
+
+Load the package by
+```
+julia> using DICOM
+```
+
+**Reading Data**
+
+Read a DICOM file by
+```
+julia> dcmData = dcm_parse("path/to/dicom/file")
+```
+The data in `dcmData` is structured as a dictionary, and individual DICOM elements can be accessed by their hex tag. 
+For example, the hex tag of "Pixel Data" is `7FE0,0010`, and it can be accessed in Julia by `dcmData[(0x7FE0,0x0010)]`. 
+
+**Writing Data**
+
+Data can be written to a DICOM file by
+```
+julia> dcm_write("path/to/output/file", dcmData)
+```
+
+**Additional Notes**
+
+DICOM files use either explicit or implicit value representation (VR). For implicit files, `DICOM.jl` will use a lookup table to guess the VR from the DICOM element's hex tag. For explicit files, `DICOM.jl` will read the VRs from the file. 
+
+- A user-defined dictionary can be supplied to override the default lookup table
+ For example, the "Instance Number" - tag `(0x0020,0x0013)` - is an integer (default VR = "IS"). We can read this as a float by setting the VR to "DS" by:
+ ```
+ myVR = Dict( (0x0020,0x0013) => "DS" )
+ dcmData = dcm_parse("path/to/dicom/file", dVR = myVR)
+ ```
+ Now `dcmData[(0x0020,0x0013)]` will return a float instead of an integer.
+
+- It is possible to skip an element by setting its VR to `""`. 
+ For example, we can skip reading the Instance Number by
+ ```
+ myVR = Dict( (0x0020,0x0013) => "" )
+ dcmData = dcm_parse("path/to/dicom/file", dVR = myVR)
+ ```
+ and now `dcmData[(0x0020,0x0013)]` will return an error because the key `(0x0020,0x0013)` doesn't exist - it was skipped during reading.
+
+- The user-supplied VR can contain a master VR with the tag `(0x0000,0x0000)` which will be used whenever `DICOM.jl` is unable to guess the VR on its own. This is convenient for reading older dicom files and skipping retired elements - i.e. where the VR lookup fails - by:
+ ```
+ myVR = Dict( (0x0000,0x0000) => "" )
+ dcmData = dcm_parse("path/to/dicom/file", dVR = myVR)
+ ```
+
+- A user-supplied VR can also be supplied during writing, e.g.:
+ ```
+ # Note that dcm_write doesn't use a named input, unlike dcm_parse with "dVR ="
+ julia> dcm_write("path/to/output/file", dcmData, dcmVR)
+ ```
+ where `dcmVR` is a dictionary which maps the hex tag to the VR.
+
+- A dictionary of VRs can be obtained by passing `true` as a 2nd argument to `dcm_parse()`, e.g.:
+ ```
+ julia> (dcmData, dcmVR) = dcm_parse("path/to/dicom/file", true)
+ ```
+ and `dcmVR` will contain a dictionary of VRs for all of the elements in `dcmData`
+