Relative data file path printing #79

tashrifbillah · 2019-01-24T20:53:52Z

Fixes #78

mf fixing

addisonElliott · 2019-01-24T23:33:50Z

We might want to add some tests to fully verify that the new parameter is working as expected.

codecov-io · 2019-01-25T02:35:13Z

Codecov Report

Merging #79 into master will not change coverage.
The diff coverage is 100%.

@@           Coverage Diff           @@
##           master      #79   +/-   ##
=======================================
  Coverage   88.12%   88.12%           
=======================================
  Files           6        6           
  Lines         362      362           
  Branches      117      117           
=======================================
  Hits          319      319           
  Misses         21       21           
  Partials       22       22

Impacted Files	Coverage Δ
nrrd/writer.py	`87.17% <100%> (ø)`	⬆️

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tashrifbillah · 2019-01-25T02:36:39Z

Added tests, two for absolute path, two for relative path. Basically, I modified the existing detached header writing tests in a clever way that encompasses new tests.

cc: @ihnorton

addisonElliott

Few minor issues, but overall I agree with what is being done.

addisonElliott · 2019-01-26T06:25:36Z

nrrd/tests/test_writing.py

@@ -158,7 +158,7 @@ def test_write_detached_raw_as_nrrd(self):
        output_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nhdr')
        output_data_filename = os.path.join(self.temp_write_dir, 'testfile_detached_raw.nrrd')

-        nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True)
+        nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True, relative_data_path= False)


Suggested change

nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True, relative_data_path= False)

nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True, relative_data_path=False)

This line is > 120 characters, can you break it at this argument. Repeat for the one other case. Remove the additional space like shown.

Sorry, never explicitly stated that the syntax is to keep lines less than 120 characters, but it's just the standard I use.

addisonElliott · 2019-01-26T06:28:59Z

nrrd/tests/test_writing.py

@@ -228,7 +228,7 @@ def test_write_detached_ascii(self):
        data, header = nrrd.read(output_filename)
        self.assertEqual(self.expected_data, data.tostring(order='F'))
        self.assertEqual(header['encoding'], 'txt')
-        self.assertEqual(header['data file'], output_data_filename)
+        self.assertEqual(header['data file'], os.path.basename(output_data_filename))


output_data_filename is equal to joined path of temp dir and the filename. We then do the basename to get the filename.

Easier if we just replace output_data_filename with the relative filename.

Repeat for above case too.

Sorry, didn't see the relative filename exists here.

addisonElliott · 2019-01-26T06:34:44Z

nrrd/writer.py

@@ -183,12 +186,12 @@ def write(filename, data, header={}, detached_header=False, custom_field_map=Non
            else:
                raise NRRDError('Invalid encoding specification while writing NRRD file: %s' % header['encoding'])

-            header['data file'] = data_filename
+            header['data file'] = os.path.basename(data_filename) if relative_data_path else os.path.abspath(data_filename)


Wrap at 120 characters please, below line is fine at just under 120.

addisonElliott · 2019-01-26T06:40:24Z

nrrd/writer.py

@@ -121,6 +121,9 @@ def write(filename, data, header={}, detached_header=False, custom_field_map=Non
        Data to save to the NRRD file
    detached_header : :obj:`bool`, optional
        Whether the header and data should be saved in separate files. Defaults to :obj:`False`
+    relative_data_path : :class:`bool`
+        whether the data file name in detached_header is saved with relative path


Line wrapped at 82 characters, only wrap at 120 characters.

Capitalize W in whether.

detached_header should be detached header because you are not referencing the boolean variable but rather the actual detached header.

I think we should include a note that this parameter is ignored if the data is attached just to be safe.

And, you say that the "data file name is saved with a relative path", but that sounds odd. The data filename isn't what is saved as a relative path, it's the data file itself.

Altogether, here's what I'm thinking. Comments welcome

Whether the data in a detached header is saved as a relative path or absolute path. This parameter is ignored if the data file is attached to the header file. Defaults to :obj:`True`

I don't think that is odd, rather the suggested one sounds like because data is not saved in the detached header. However, counter suggestion combining with yours:

Whether the data file name in detached header is saved with a relative path or absolute path.
This parameter is ignored if there is no detached header. Defaults to :obj:True

PR is ready, let me know your final thoughts on this.

addisonElliott

Few more minor changes, sorry!

In addition, do you mind just quickly reviewing my other PRs. Look for any issues you may see with the code. I should've split it up into multiple PRs but it was just a spring cleaning type of thing.

addisonElliott · 2019-01-26T15:05:54Z

nrrd/tests/test_writing.py

@@ -228,7 +230,7 @@ def test_write_detached_ascii(self):
        data, header = nrrd.read(output_filename)


Sorry, one small thing. Since you directly placed the string to be asserted, the output_data_filename variable is not used. Remove that please

Same for above.

Will review your other PRs, but may take some time.

addisonElliott · 2019-01-26T15:07:31Z

nrrd/writer.py

@@ -121,6 +121,9 @@ def write(filename, data, header={}, detached_header=False, custom_field_map=Non
        Data to save to the NRRD file
    detached_header : :obj:`bool`, optional
        Whether the header and data should be saved in separate files. Defaults to :obj:`False`
+    relative_data_path : :class:`bool`
+        Whether the data file name in detached header is saved with a relative path or absolute path.


Alright, rereading this now I agree with how it's set.

Just one minor thing, I usually prefer the use of filename rather than file name. To stay consistent let's change it. I think I have it without the space in the docs and such.

Suggested change

Whether the data file name in detached header is saved with a relative path or absolute path.

Whether the data filename in detached header is saved with a relative path or absolute path.

addisonElliott · 2019-01-26T16:51:56Z

@tashrifbillah No problem, we're all busy so I understand if it takes you some time.

tashrifbillah and others added 3 commits January 24, 2019 11:12

Merge pull request #1 from mhe/master

d590ed4

mf fixing

relative data path

bfc7db9

relative data path

362612b

relative path test

106d2f7

addisonElliott requested changes Jan 26, 2019

View reviewed changes

tashrifbillah added 2 commits January 26, 2019 09:38

using relative filename

ae816aa

wrapping lines at 120 characters

524100f

addisonElliott requested changes Jan 26, 2019

View reviewed changes

tashrifbillah added 2 commits January 26, 2019 10:56

filename instead of file name

fcb53fa

unused variable removal

d820b43

addisonElliott merged commit 017a905 into mhe:master Jan 26, 2019

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Relative data file path printing #79

Relative data file path printing #79

tashrifbillah commented Jan 24, 2019

addisonElliott commented Jan 24, 2019

codecov-io commented Jan 25, 2019 •

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addisonElliott commented Jan 26, 2019

	nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True, relative_data_path= False)
	nrrd.write(output_data_filename, self.data_input, {u'encoding': 'raw'}, detached_header=True, relative_data_path=False)

		@@ -228,7 +230,7 @@ def test_write_detached_ascii(self):
		data, header = nrrd.read(output_filename)

	Whether the data file name in detached header is saved with a relative path or absolute path.
	Whether the data filename in detached header is saved with a relative path or absolute path.

Relative data file path printing #79

Relative data file path printing #79

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tashrifbillah commented Jan 24, 2019

addisonElliott commented Jan 24, 2019

codecov-io commented Jan 25, 2019 • edited Loading

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addisonElliott commented Jan 26, 2019

codecov-io commented Jan 25, 2019 •

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tashrifbillah commented Jan 25, 2019 •

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