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Gabriel-p opened this issue Feb 21, 2014 · 6 comments · Fixed by #16650
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genfromtxt won't unpack if dtype=None #4341

Gabriel-p opened this issue Feb 21, 2014 · 6 comments · Fixed by #16650
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00 - Bug component: numpy.lib
Milestone
1.20.0 release

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@Gabriel-p
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Not sure if this is a bug or a feature but if I use:

f_data = np.genfromtxt('file.dat', dtype=None, unpack=True)

where file.dat is a standard data file with several columns (ie: http://pastebin.com/ihEW2dxS) the result is not transposed as one would expect having set unpack=True.

For example, the line f_data = np.loadtxt('file.dat', unpack=True) works as expected.
@charris
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charris commented Feb 24, 2014

Looks like a bug, marking it so until informed otherwise.

@ddasilva
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ddasilva commented Mar 3, 2014

I investigated this a little bit.

The result of @Gabriel-p's code is a shape (12,) flex array. The code calls output.T on it, but since it's one dimensional this is a no-op.

The biggest issue that dtype=None specifies that it will be flex array. Each column has a separate inferred type. If we were to truly transpose this result, each row would need to have a separate type. AFAIK, the only way to do that is to have a list or tuple of homogeneous arrays.

Since numCols << numRows in the text file, using a list or tuple shouldn't be a big deal. If implemented that way, it would unpack for x, y, z = np.genfromtxt(...) as specified in the docs, and solve @Gabriel-p's case.

However, genfromtxt is already over 600 lines. Any thoughts?

@hsgg
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hsgg commented May 16, 2014

Just got bitten by this, too. I made a test case, see

https://github.com/hsgg/numpy.git

@moi90
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moi90 commented Dec 22, 2017 •
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I also experience this. loadtxt is a bit more clever:

if unpack:
        if len(dtype_types) > 1:
            # For structured arrays, return an array for each field.
            return [X[field] for field in dtype.names]
        else:
            return X.T

Why doesn't genfromtxt do this?

@adehecq
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adehecq commented Jun 10, 2020

Any update on this issue? It seems like it hasn't changed since 2014.

@WarrenWeckesser
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WarrenWeckesser commented Jun 10, 2020 •
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The suggestion @moi90 made a couple years ago is correct. genfromtxt should do the same thing as loadtxt.

I think it will be easy to fix, so I've tagged the issue as a "good first issue".

@WarrenWeckesser WarrenWeckesser added this to the 1.20.0 release milestone Jun 10, 2020
@AndrewEckart AndrewEckart mentioned this issue Jun 20, 2020
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AndrewEckart added a commit to AndrewEckart/numpy that referenced this issue Jul 12, 2020
@AndrewEckart
ENH: Allow genfromtxt to unpack structured arrays
189ad50 
Previously, `genfromtxt` failed to transpose its output when
`unpack=True` and `dtype` was structured (or `dtype=None` and the
inferred `dtype` was structured). This patch resolves the issue by
returning a list of arrays, as in `loadtxt`. Includes tests and updates
the docstring to match `loadtxt`.

Fixes numpy#4341
@mzechmeister mzechmeister mentioned this issue Mar 14, 2021
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@emirkmo emirkmo mentioned this issue Jan 19, 2022
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ENH: Allow genfromtxt to unpack structured arrays AndrewEckart/numpy
8 participants
@charris @hsgg @WarrenWeckesser @moi90 @ddasilva @mattip @adehecq @Gabriel-p
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