Allow override of dup. field error, and zlib compression level

[ihnorton]

• Allow override of duplicate field error, with a warning instead (occasionally occur with buggy writers)

• Allow changing the compression level - can significantly improve write performance at minimal space cost. As an illustrative example:

timing test details

```python import nrrd nrrd.reader._NRRD_ALLOW_DUPLICATE_FIELD = True ``` ```python img,hdr = nrrd.read("/path/to/dwi.nhdr") %timeit -n1 -r1 nrrd.write("test.nrrd", img, hdr) ``` 193 ms ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each) ```python hdr['encoding'] = 'gz' %timeit -n1 -r1 nrrd.write("test_zl_9.nrrd", img, hdr) ``` 20.2 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each) ```python nrrd.writer._ZLIB_LEVEL = -1 hdr['encoding'] = 'gz' %timeit -n1 -r1 nrrd.write("test_zl_default.nrrd", img, hdr) ``` 9.94 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each) ```python nrrd.writer._ZLIB_LEVEL = 1 hdr['encoding'] = 'gz' %timeit -n1 -r1 nrrd.write("test_zl_1.nrrd", img, hdr) ``` 2.68 s ± 0 ns per loop (mean ± std. dev. of 1 run, 1 loop each)

Output files below (test.nrrd is original, and zl_default is roughly level 6 per the docs):

!ls -lah *.nrrd

    -rw-r--r--  1 inorton  staff    61M Aug 24 16:38 test.nrrd
    -rw-r--r--  1 inorton  staff    27M Aug 24 16:39 test_zl_1.nrrd
    -rw-r--r--  1 inorton  staff    26M Aug 24 16:38 test_zl_9.nrrd
    -rw-r--r--  1 inorton  staff    26M Aug 24 16:38 test_zl_default.nrrd

So, level 9 is ~10x slower than level 1, but saves only 1 MB. This is brain MRI data.

[codecov-io]

Codecov Report

Merging #65 into master will increase coverage by 0.74%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #65      +/-   ##
==========================================
+ Coverage   86.64%   87.39%   +0.74%     
==========================================
  Files           6        6              
  Lines         352      357       +5     
  Branches      113      114       +1     
==========================================
+ Hits          305      312       +7     
+ Misses         23       22       -1     
+ Partials       24       23       -1

Impacted Files	Coverage Δ
nrrd/writer.py	87.17% <100%> (ø)	:arrow_up:
nrrd/reader.py	81.98% <100%> (+1.85%)	:arrow_up:

---

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[ihnorton]

Also, issue with Travis failing on Python 2.7, need to resolve this as well.

Addressed.

I would make these parameters as apart of the read function instead.

I made the compression level a parameter of write and added the docstring. But the field error override is kind of odd/special, and violates the nrrd spec, so it probably shouldn't be advertised.

[codecov-io]

Codecov Report

Merging #65 into master will increase coverage by 0.74%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master      #65      +/-   ##
==========================================
+ Coverage   86.64%   87.39%   +0.74%     
==========================================
  Files           6        6              
  Lines         352      357       +5     
  Branches      113      114       +1     
==========================================
+ Hits          305      312       +7     
+ Misses         23       22       -1     
+ Partials       24       23       -1

Impacted Files	Coverage Δ
nrrd/reader.py	81.98% <100%> (+1.85%)	:arrow_up:
nrrd/writer.py	87.17% <100%> (ø)	:arrow_up:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update caf8506...77d5d2c. Read the comment docs.

[ihnorton]

Right now it overwrites and saves the last field given. Is this the best way to handle it?

Yes

Also, I was thinking maybe it would be worthwhile to write a test for testing the compression on gzip and bzip2. My thoughts are to set the compression level to something besides 9 for both of these and then test the file size is a certain size?

Done. For now I commented out the assert about file size difference for bz2, because for the binary ball data, output is the same size at all levels.

[addisonElliott]

LGTM 👍

I guess I wasn't fully thinking of the application for the duplicate field section. I think I agree that it should not be a function parameter in read or read_header.

The tests look good!

[ihnorton]

Thanks!