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Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 7
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From: David R. <dav...@gm...> - 2013-02-04 15:54:22
|
Hi Josh,
Here is my __iter__ code:
def __iter__(self):
table = self.table
itemsize = self.dtype.itemsize
nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE'] // itemsize
max_row = len(self)
for start_row in xrange(0, len(self), nrowsinbuf):
end_row = min([start_row + nrowsinbuf, max_row])
buf = table.read(start_row, end_row, 1, field=self.pathname)
for row in buf:
yield row
It does look different, I will try swapping in the code from github and see
what happens.
On Mon, Feb 4, 2013 at 9:59 AM, <
pyt...@li...> wrote:
> Send Pytables-users mailing list submissions to
> pyt...@li...
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://lists.sourceforge.net/lists/listinfo/pytables-users
> or, via email, send a message with subject or body 'help' to
> pyt...@li...
>
> You can reach the person managing the list at
> pyt...@li...
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Pytables-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Pytables-users Digest, Vol 81, Issue 4 (Josh Ayers)
> 2. Re: Pytables-users Digest, Vol 81, Issue 6 (David Reed)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 1 Feb 2013 14:08:47 -0800
> From: Josh Ayers <jos...@gm...>
> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 4
> To: Discussion list for PyTables
> <pyt...@li...>
> Message-ID:
> <CACOB4aPG4NZ6b2a3v=
> 1Ue...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> David,
>
> You added a custom version of table.Column.__iter__, correct? Could you
> also include that along with the script to reproduce the error?
>
> It seems like the problem may be in the 'nrowsinbuf' calculation - see
> [1]. Each of your rows is 17 x 9600 = 163200 bytes. If you're using the
> default 1MB value for IO_BUFFER_SIZE, it should be reading in rows of 6
> chunks. Instead, it's reading the entire table.
>
> [1]:
> https://github.com/PyTables/PyTables/blob/develop/tables/table.py#L3296
>
>
>
> On Fri, Feb 1, 2013 at 1:50 PM, Anthony Scopatz <sc...@gm...> wrote:
>
> >
> >
> > On Fri, Feb 1, 2013 at 3:27 PM, David Reed <dav...@gm...>
> wrote:
> >
> >> at the error:
> >>
> >> result = numpy.empty(shape=nrows, dtype=dtypeField)
> >>
> >> nrows = 4620 and dtypeField is ('bool', (17, 9600))
> >>
> >> I'm not sure what that means as a dtype, but thats what it is.
> >>
> >> Forgive me if I'm being totally naive, but I thought the whole point of
> >> __iter__ with pyttables was to do iteration on the fly, so there is no
> >> preallocation.
> >>
> >
> > Nope you are not being naive at all. That is the point.
> >
> >
> >> If you have any ideas on this I'm all ears.
> >>
> >
> > If you could send a minimal script which reproduces this error, that
> would
> > help a lot.
> >
> > Be Well
> > Anthony
> >
> >
> >>
> >>
> >> Thanks again.
> >>
> >> Dave
> >>
> >>
> >> On Fri, Feb 1, 2013 at 3:45 PM, <
> >> pyt...@li...> wrote:
> >>
> >>> Send Pytables-users mailing list submissions to
> >>> pyt...@li...
> >>>
> >>> To subscribe or unsubscribe via the World Wide Web, visit
> >>> https://lists.sourceforge.net/lists/listinfo/pytables-users
> >>> or, via email, send a message with subject or body 'help' to
> >>> pyt...@li...
> >>>
> >>> You can reach the person managing the list at
> >>> pyt...@li...
> >>>
> >>> When replying, please edit your Subject line so it is more specific
> >>> than "Re: Contents of Pytables-users digest..."
> >>>
> >>>
> >>> Today's Topics:
> >>>
> >>> 1. Re: Pytables-users Digest, Vol 81, Issue 2 (Anthony Scopatz)
> >>>
> >>>
> >>> ----------------------------------------------------------------------
> >>>
> >>> Message: 1
> >>> Date: Fri, 1 Feb 2013 14:44:40 -0600
> >>> From: Anthony Scopatz <sc...@gm...>
> >>> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 2
> >>> To: Discussion list for PyTables
> >>> <pyt...@li...>
> >>> Message-ID:
> >>> <
> >>> CAP...@ma...>
> >>> Content-Type: text/plain; charset="iso-8859-1"
> >>>
> >>> On Fri, Feb 1, 2013 at 12:43 PM, David Reed <dav...@gm...>
> >>> wrote:
> >>>
> >>> > Hi Anthony,
> >>> >
> >>> > Thanks for the reply.
> >>> >
> >>> > I honestly don't know how to monitor my Python memory usage, but I'm
> >>> sure
> >>> > that its caused by out of memory.
> >>> >
> >>>
> >>> Well, I would just run top or process monitor or something while
> running
> >>> the python script to see what happens to memory usage as the script
> chugs
> >>> along...
> >>>
> >>>
> >>> > I'm just trying to find out how to fix it. My HDF5 table has 4620
> >>> rows
> >>> > and the column I'm iterating over is a 17x9600 boolean matrix. The
> >>> > __iter__ method is preallocating an array that is this size which
> >>> appears
> >>> > to be root of the error. I was hoping there is a fix somewhere in
> >>> here to
> >>> > not have to do this preallocation.
> >>> >
> >>>
> >>> So a 17x9600 boolean matrix should only be 0.155 MB in space. 4620 of
> >>> these is ~760 MB. If you have 2 GB of memory and you are iterating
> over
> >>> 2
> >>> of these (templates & masks) it is conceivable that you are just
> running
> >>> out of memory. Maybe there is a way that __iter__ could not
> preallocate
> >>> something that is basically a temporary. What is the dtype of the
> >>> templates array?
> >>>
> >>> Be Well
> >>> Anthony
> >>>
> >>>
> >>> >
> >>> > Thanks again.
> >>>
> >>>
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Mon, 4 Feb 2013 09:58:53 -0500
> From: David Reed <dav...@gm...>
> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 6
> To: pyt...@li...
> Message-ID:
> <CAM6XA7=
> h50...@ma...>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Anthony,
>
> Sorry to just get back to you. I can send a script, should I send a script
> that creates some fake data as well?
>
> -Dave
>
>
> On Fri, Feb 1, 2013 at 4:50 PM, <
> pyt...@li...> wrote:
>
> > Send Pytables-users mailing list submissions to
> > pyt...@li...
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > https://lists.sourceforge.net/lists/listinfo/pytables-users
> > or, via email, send a message with subject or body 'help' to
> > pyt...@li...
> >
> > You can reach the person managing the list at
> > pyt...@li...
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pytables-users digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: Pytables-users Digest, Vol 81, Issue 4 (Anthony Scopatz)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 1 Feb 2013 15:50:11 -0600
> > From: Anthony Scopatz <sc...@gm...>
> > Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 4
> > To: Discussion list for PyTables
> > <pyt...@li...>
> > Message-ID:
> > <
> > CAP...@ma...>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > On Fri, Feb 1, 2013 at 3:27 PM, David Reed <dav...@gm...>
> wrote:
> >
> > > at the error:
> > >
> > > result = numpy.empty(shape=nrows, dtype=dtypeField)
> > >
> > > nrows = 4620 and dtypeField is ('bool', (17, 9600))
> > >
> > > I'm not sure what that means as a dtype, but thats what it is.
> > >
> > > Forgive me if I'm being totally naive, but I thought the whole point of
> > > __iter__ with pyttables was to do iteration on the fly, so there is no
> > > preallocation.
> > >
> >
> > Nope you are not being naive at all. That is the point.
> >
> >
> > > If you have any ideas on this I'm all ears.
> > >
> >
> > If you could send a minimal script which reproduces this error, that
> would
> > help a lot.
> >
> > Be Well
> > Anthony
> >
> >
> > >
> > >
> > > Thanks again.
> > >
> > > Dave
> > >
> > >
> > > On Fri, Feb 1, 2013 at 3:45 PM, <
> > > pyt...@li...> wrote:
> > >
> > >> Send Pytables-users mailing list submissions to
> > >> pyt...@li...
> > >>
> > >> To subscribe or unsubscribe via the World Wide Web, visit
> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> or, via email, send a message with subject or body 'help' to
> > >> pyt...@li...
> > >>
> > >> You can reach the person managing the list at
> > >> pyt...@li...
> > >>
> > >> When replying, please edit your Subject line so it is more specific
> > >> than "Re: Contents of Pytables-users digest..."
> > >>
> > >>
> > >> Today's Topics:
> > >>
> > >> 1. Re: Pytables-users Digest, Vol 81, Issue 2 (Anthony Scopatz)
> > >>
> > >>
> > >> ----------------------------------------------------------------------
> > >>
> > >> Message: 1
> > >> Date: Fri, 1 Feb 2013 14:44:40 -0600
> > >> From: Anthony Scopatz <sc...@gm...>
> > >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 81, Issue 2
> > >> To: Discussion list for PyTables
> > >> <pyt...@li...>
> > >> Message-ID:
> > >> <
> > >> CAP...@ma...>
> > >> Content-Type: text/plain; charset="iso-8859-1"
> > >>
> > >> On Fri, Feb 1, 2013 at 12:43 PM, David Reed <dav...@gm...>
> > >> wrote:
> > >>
> > >> > Hi Anthony,
> > >> >
> > >> > Thanks for the reply.
> > >> >
> > >> > I honestly don't know how to monitor my Python memory usage, but I'm
> > >> sure
> > >> > that its caused by out of memory.
> > >> >
> > >>
> > >> Well, I would just run top or process monitor or something while
> running
> > >> the python script to see what happens to memory usage as the script
> > chugs
> > >> along...
> > >>
> > >>
> > >> > I'm just trying to find out how to fix it. My HDF5 table has 4620
> > rows
> > >> > and the column I'm iterating over is a 17x9600 boolean matrix. The
> > >> > __iter__ method is preallocating an array that is this size which
> > >> appears
> > >> > to be root of the error. I was hoping there is a fix somewhere in
> > here
> > >> to
> > >> > not have to do this preallocation.
> > >> >
> > >>
> > >> So a 17x9600 boolean matrix should only be 0.155 MB in space. 4620 of
> > >> these is ~760 MB. If you have 2 GB of memory and you are iterating
> > over 2
> > >> of these (templates & masks) it is conceivable that you are just
> running
> > >> out of memory. Maybe there is a way that __iter__ could not
> preallocate
> > >> something that is basically a temporary. What is the dtype of the
> > >> templates array?
> > >>
> > >> Be Well
> > >> Anthony
> > >>
> > >>
> > >> >
> > >> > Thanks again.
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > On Fri, Feb 1, 2013 at 11:12 AM, <
> > >> > pyt...@li...> wrote:
> > >> >
> > >> >> Send Pytables-users mailing list submissions to
> > >> >> pyt...@li...
> > >> >>
> > >> >> To subscribe or unsubscribe via the World Wide Web, visit
> > >> >>
> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> or, via email, send a message with subject or body 'help' to
> > >> >> pyt...@li...
> > >> >>
> > >> >> You can reach the person managing the list at
> > >> >> pyt...@li...
> > >> >>
> > >> >> When replying, please edit your Subject line so it is more specific
> > >> >> than "Re: Contents of Pytables-users digest..."
> > >> >>
> > >> >>
> > >> >> Today's Topics:
> > >> >>
> > >> >> 1. Re: Pytables-users Digest, Vol 80, Issue 9 (Anthony Scopatz)
> > >> >>
> > >> >>
> > >> >>
> > ----------------------------------------------------------------------
> > >> >>
> > >> >> Message: 1
> > >> >> Date: Fri, 1 Feb 2013 10:11:47 -0600
> > >> >> From: Anthony Scopatz <sc...@gm...>
> > >> >> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 80, Issue
> 9
> > >> >> To: Discussion list for PyTables
> > >> >> <pyt...@li...>
> > >> >> Message-ID:
> > >> >> <
> > >> >> CAP...@ma...
> >
> > >> >> Content-Type: text/plain; charset="iso-8859-1"
> > >> >>
> > >> >> Hi David,
> > >> >>
> > >> >> Sorry, I haven't had a ton of time recently. You seem to be
> getting
> > a
> > >> >> memory error on creating a numpy array. This kind of thing
> typically
> > >> >> happens when you are out of memory. Does this seem to be the case
> > with
> > >> >> you? When this dies, is your memory usage at 100%? If so, this
> > >> algorithm
> > >> >> might require a little tweaking...
> > >> >>
> > >> >> Be Well
> > >> >> Anthony
> > >> >>
> > >> >>
> > >> >> On Fri, Feb 1, 2013 at 6:15 AM, David Reed <dav...@gm...
> >
> > >> >> wrote:
> > >> >>
> > >> >> > I'm still having problems with this one. I can't tell if this
> > >> something
> > >> >> > dumb Im doing with itertools, or if its something in pytables.
> > >> >> >
> > >> >> > Would appreciate any help.
> > >> >> >
> > >> >> > Thanks
> > >> >> >
> > >> >> >
> > >> >> > On Wed, Jan 30, 2013 at 5:00 PM, David Reed <
> > dav...@gm...
> > >> >> >wrote:
> > >> >> >
> > >> >> >> I think I have to reopen this issue. I have been running fine
> for
> > >> >> awhile
> > >> >> >> using the combinations method from itertools, but have recently
> > run
> > >> >> into a
> > >> >> >> memory since I have recently quadrupled the size of the hdf
> file.
> > >> >> >>
> > >> >> >> Here is my code again:
> > >> >> >>
> > >> >> >> from itertools import combinations, izip
> > >> >> >> with tb.openFile(h5_all, 'r') as f:
> > >> >> >> irises = f.root.irises
> > >> >> >>
> > >> >> >> templates = f.root.irises.cols.templates
> > >> >> >> masks = f.root.irises.cols.masks1
> > >> >> >>
> > >> >> >> N_irises = len(irises)
> > >> >> >> index = np.ones((20 * 480), np.bool)
> > >> >> >>
> > >> >> >> print '%i Comparisons' % (N_irises*(N_irises - 1)/2)
> > >> >> >> D = np.empty((N_irises, N_irises))
> > >> >> >> for (t1, m1, ii), (t2, m2, jj) in combinations(izip(templates,
> > >> masks,
> > >> >> >> range(N_irises)), 2):
> > >> >> >> # print ii
> > >> >> >> D[ii, jj] = ham_dist(
> > >> >> >> t1[8, index],
> > >> >> >> t2[:, index],
> > >> >> >> m1[8, index],
> > >> >> >> m2[:, index],
> > >> >> >> )
> > >> >> >>
> > >> >> >> And here is the error:
> > >> >> >>
> > >> >> >> In [10]: get_hd3()
> > >> >> >> 10669890 Comparisons
> > >> >> >>
> > >> >> >>
> > >> >>
> > >>
> >
> ---------------------------------------------------------------------------
> > >> >> >> MemoryError Traceback (most recent
> > >> call
> > >> >> >> last)
> > >> >> >> <ipython-input-10-cfb255ce7bd1> in <module>()
> > >> >> >> ----> 1 get_hd3()
> > >> >> >>
> > >> >> >>
> > >> >> >> 118 print '%i Comparisons' %
> > >> (N_irises*(N_irises -
> > >> >> >> 1)/2)
> > >> >> >> 119 D = np.empty((N_irises, N_irises))
> > >> >> >> --> 120 for (t1, m1, ii), (t2, m2, jj) in
> > >> >> >> combinations(izip(temp
> > >> >> >> lates, masks, range(N_irises)), 2):
> > >> >> >> 121 # print ii
> > >> >> >> 122 D[ii, jj] = ham_dist(
> > >> >> >>
> > >> >> >> c:\python27\lib\site-packages\tables\table.pyc in __iter__(self)
> > >> >> >> 3274 for start_row in xrange(0, len(self),
> nrowsinbuf):
> > >> >> >> 3275 end_row = min([start_row + nrowsinbuf,
> > max_row])
> > >> >> >> -> 3276 buf = table.read(start_row, end_row, 1,
> > >> >> >> field=self.pathname)
> > >> >> >>
> > >> >> >> 3277 for row in buf:
> > >> >> >> 3278 yield row
> > >> >> >>
> > >> >> >> c:\python27\lib\site-packages\tables\table.pyc in read(self,
> > start,
> > >> >> stop,
> > >> >> >> step,
> > >> >> >> field)
> > >> >> >> 1772 (start, stop, step) =
> > self._processRangeRead(start,
> > >> >> stop,
> > >> >> >> step)
> > >> >> >> 1773
> > >> >> >> -> 1774 arr = self._read(start, stop, step, field)
> > >> >> >> 1775 return internal_to_flavor(arr, self.flavor)
> > >> >> >> 1776
> > >> >> >>
> > >> >> >> c:\python27\lib\site-packages\tables\table.pyc in _read(self,
> > start,
> > >> >> >> stop, step,
> > >> >> >> field)
> > >> >> >> 1719 if field:
> > >> >> >> 1720 # Create a container for the results
> > >> >> >> -> 1721 result = numpy.empty(shape=nrows,
> > >> dtype=dtypeField)
> > >> >> >> 1722 else:
> > >> >> >> 1723 # Recarray case
> > >> >> >>
> > >> >> >> MemoryError:
> > >> >> >> > c:\python27\lib\site-packages\tables\table.py(1721)_read()
> > >> >> >> 1720 # Create a container for the results
> > >> >> >> -> 1721 result = numpy.empty(shape=nrows,
> > >> dtype=dtypeField)
> > >> >> >> 1722 else:
> > >> >> >>
> > >> >> >> Also, if you guys see any performance problems in my code,
> please
> > >> let
> > >> >> me
> > >> >> >> know.
> > >> >> >>
> > >> >> >> Thank you so much for the help.
> > >> >> >>
> > >> >> >> -Dave
> > >> >> >>
> > >> >> >>
> > >> >> >> On Fri, Jan 4, 2013 at 8:57 AM, <
> > >> >> >> pyt...@li...> wrote:
> > >> >> >>
> > >> >> >>> Send Pytables-users mailing list submissions to
> > >> >> >>> pyt...@li...
> > >> >> >>>
> > >> >> >>> To subscribe or unsubscribe via the World Wide Web, visit
> > >> >> >>>
> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> or, via email, send a message with subject or body 'help' to
> > >> >> >>> pyt...@li...
> > >> >> >>>
> > >> >> >>> You can reach the person managing the list at
> > >> >> >>> pyt...@li...
> > >> >> >>>
> > >> >> >>> When replying, please edit your Subject line so it is more
> > specific
> > >> >> >>> than "Re: Contents of Pytables-users digest..."
> > >> >> >>>
> > >> >> >>>
> > >> >> >>> Today's Topics:
> > >> >> >>>
> > >> >> >>> 1. Re: Pytables-users Digest, Vol 80, Issue 8 (David Reed)
> > >> >> >>>
> > >> >> >>>
> > >> >> >>>
> > >> ----------------------------------------------------------------------
> > >> >> >>>
> > >> >> >>> Message: 1
> > >> >> >>> Date: Fri, 4 Jan 2013 08:56:28 -0500
> > >> >> >>> From: David Reed <dav...@gm...>
> > >> >> >>> Subject: Re: [Pytables-users] Pytables-users Digest, Vol 80,
> > Issue
> > >> 8
> > >> >> >>> To: pyt...@li...
> > >> >> >>> Message-ID:
> > >> >> >>> <
> > >> >> >>>
> > CAM...@ma...
> > >> >
> > >> >> >>> Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>>
> > >> >> >>> I can't thank you guys enough for the help. I was able to add
> > the
> > >> >> >>> __iter__
> > >> >> >>> function to the table.py file and everything seems to be
> working
> > >> >> great!
> > >> >> >>> I'm not quite as fast as I was with iterating right of a
> matrix
> > >> but
> > >> >> >>> pretty
> > >> >> >>> close. I was at 555 comparisons per second, and now im at 420.
> > >> >> >>>
> > >> >> >>> I handled the problem I mentioned earlier by doing this, and it
> > >> seems
> > >> >> to
> > >> >> >>> work great:
> > >> >> >>>
> > >> >> >>> A = f.root.data.cols.A
> > >> >> >>> B = f.root.data.cols.B
> > >> >> >>>
> > >> >> >>> D = np.empty((len(A), len(A))
> > >> >> >>> for (a1, b1, ii), (a2, b2, jj) in combinations(izip(A, B,
> > >> >> range(len(A))),
> > >> >> >>> 2):
> > >> >> >>> D[ii, jj] = compare(a1, a2, b1, b2)
> > >> >> >>>
> > >> >> >>> Again, thanks a lot.
> > >> >> >>>
> > >> >> >>> -Dave
> > >> >> >>>
> > >> >> >>>
> > >> >> >>> On Thu, Jan 3, 2013 at 6:31 PM, <
> > >> >> >>> pyt...@li...> wrote:
> > >> >> >>>
> > >> >> >>> > Send Pytables-users mailing list submissions to
> > >> >> >>> > pyt...@li...
> > >> >> >>> >
> > >> >> >>> > To subscribe or unsubscribe via the World Wide Web, visit
> > >> >> >>> >
> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > or, via email, send a message with subject or body 'help' to
> > >> >> >>> > pyt...@li...
> > >> >> >>> >
> > >> >> >>> > You can reach the person managing the list at
> > >> >> >>> > pyt...@li...
> > >> >> >>> >
> > >> >> >>> > When replying, please edit your Subject line so it is more
> > >> specific
> > >> >> >>> > than "Re: Contents of Pytables-users digest..."
> > >> >> >>> >
> > >> >> >>> >
> > >> >> >>> > Today's Topics:
> > >> >> >>> >
> > >> >> >>> > 1. Re: Pytables-users Digest, Vol 80, Issue 3 (Anthony
> > >> Scopatz)
> > >> >> >>> > 2. Re: Pytables-users Digest, Vol 80, Issue 4 (Anthony
> > >> Scopatz)
> > >> >> >>> >
> > >> >> >>> >
> > >> >> >>> >
> > >> >>
> > ----------------------------------------------------------------------
> > >> >> >>> >
> > >> >> >>> > Message: 1
> > >> >> >>> > Date: Thu, 3 Jan 2013 17:26:55 -0600
> > >> >> >>> > From: Anthony Scopatz <sc...@gm...>
> > >> >> >>> > Subject: Re: [Pytables-users] Pytables-users Digest, Vol 80,
> > >> Issue 3
> > >> >> >>> > To: Discussion list for PyTables
> > >> >> >>> > <pyt...@li...>
> > >> >> >>> > Message-ID:
> > >> >> >>> > <CAPk-6T6sz=J5ay_a9YGLPe_yBLGa9c+XgxG0CRNs6fJ=
> > >> >> >>> > Gz...@ma...>
> > >> >> >>> > Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> >
> > >> >> >>> > On Thu, Jan 3, 2013 at 2:17 PM, David Reed <
> > >> dav...@gm...>
> > >> >> >>> wrote:
> > >> >> >>> >
> > >> >> >>> > > Thanks a lot for the help so far guys!
> > >> >> >>> > >
> > >> >> >>> > > Looking at itertools, I found what I believe to be the
> > perfect
> > >> >> >>> function
> > >> >> >>> > > for what I need, itertools.combinations. This appears to
> be a
> > >> >> valid
> > >> >> >>> > > replacement to the method proposed.
> > >> >> >>> > >
> > >> >> >>> >
> > >> >> >>> > Yes, combinations is awesome!
> > >> >> >>> >
> > >> >> >>> >
> > >> >> >>> > >
> > >> >> >>> > > There is a small problem that I didn't mention is that my
> > >> compare
> > >> >> >>> > function
> > >> >> >>> > > actually takes as inputs 2 columns from the table. Like so:
> > >> >> >>> > >
> > >> >> >>> > > D = np.empty((N_irises, N_irises))
> > >> >> >>> > > for ii in xrange(N_elements):
> > >> >> >>> > > for jj in xrange(ii+1, N_elements):
> > >> >> >>> > > D[ii, jj] = compare(data['element1'][ii],
> > >> >> >>> > data['element1'][jj],data['element2'][ii],
> > >> >> >>> > > data['element2'][jj])
> > >> >> >>> > >
> > >> >> >>> > > Is there an efficient way of using itertools with this
> > >> structure?
> > >> >> >>> > >
> > >> >> >>> >
> > >> >> >>> > You can always make two other iterators for each column.
> Since
> > >> you
> > >> >> >>> have
> > >> >> >>> > two columns you would have 4 iterators. I am not sure how
> fast
> > >> >> this is
> > >> >> >>> > going to be but I am confident that there is definitely a way
> > to
> > >> do
> > >> >> >>> this in
> > >> >> >>> > one for-loop, which is going to be way faster than nested
> > loops.
> > >> >> >>> >
> > >> >> >>> > Be Well
> > >> >> >>> > Anthony
> > >> >> >>> >
> > >> >> >>> >
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > > On Thu, Jan 3, 2013 at 1:29 PM, <
> > >> >> >>> > > pyt...@li...> wrote:
> > >> >> >>> > >
> > >> >> >>> > >> Send Pytables-users mailing list submissions to
> > >> >> >>> > >> pyt...@li...
> > >> >> >>> > >>
> > >> >> >>> > >> To subscribe or unsubscribe via the World Wide Web, visit
> > >> >> >>> > >>
> > >> >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >> or, via email, send a message with subject or body 'help'
> to
> > >> >> >>> > >> pyt...@li...
> > >> >> >>> > >>
> > >> >> >>> > >> You can reach the person managing the list at
> > >> >> >>> > >> pyt...@li...
> > >> >> >>> > >>
> > >> >> >>> > >> When replying, please edit your Subject line so it is more
> > >> >> specific
> > >> >> >>> > >> than "Re: Contents of Pytables-users digest..."
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >> Today's Topics:
> > >> >> >>> > >>
> > >> >> >>> > >> 1. Re: Nested Iteration of HDF5 using PyTables (Josh
> > Ayers)
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>>
> > >> ----------------------------------------------------------------------
> > >> >> >>> > >>
> > >> >> >>> > >> Message: 1
> > >> >> >>> > >> Date: Thu, 3 Jan 2013 10:29:33 -0800
> > >> >> >>> > >> From: Josh Ayers <jos...@gm...>
> > >> >> >>> > >> Subject: Re: [Pytables-users] Nested Iteration of HDF5
> using
> > >> >> >>> PyTables
> > >> >> >>> > >> To: Discussion list for PyTables
> > >> >> >>> > >> <pyt...@li...>
> > >> >> >>> > >> Message-ID:
> > >> >> >>> > >> <
> > >> >> >>> > >>
> > >> >> CAC...@ma...
> >
> > >> >> >>> > >> Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> > >>
> > >> >> >>> > >> David,
> > >> >> >>> > >>
> > >> >> >>> > >> The change in issue 27 was only for iteration over a
> > >> >> tables.Column
> > >> >> >>> > >> instance. To use it, tweak Anthony's code as follows.
> This
> > >> will
> > >> >> >>> > iterate
> > >> >> >>> > >> over the "element" column, as in your original example.
> > >> >> >>> > >>
> > >> >> >>> > >> Note also that this will only work with the development
> > >> version
> > >> >> of
> > >> >> >>> > >> PyTables
> > >> >> >>> > >> available on github. It will be very slow using the
> > released
> > >> >> >>> v2.4.0.
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >> from itertools import izip
> > >> >> >>> > >>
> > >> >> >>> > >> with tb.openFile(...) as f:
> > >> >> >>> > >> data = f.root.data.cols.element
> > >> >> >>> > >> data_i = iter(data)
> > >> >> >>> > >> data_j = iter(data)
> > >> >> >>> > >> data_i.next() # throw the first value away
> > >> >> >>> > >> for i, j in izip(data_i, data_j):
> > >> >> >>> > >> compare(i, j)
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >> Hope that helps,
> > >> >> >>> > >> Josh
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >> On Thu, Jan 3, 2013 at 9:11 AM, Anthony Scopatz <
> > >> >> sc...@gm...>
> > >> >> >>> > >> wrote:
> > >> >> >>> > >>
> > >> >> >>> > >> > HI David,
> > >> >> >>> > >> >
> > >> >> >>> > >> > Tables and table column iteration have been overhauled
> > >> fairly
> > >> >> >>> recently
> > >> >> >>> > >> > [1]. So you might try creating two iterators, offset by
> > >> one,
> > >> >> and
> > >> >> >>> then
> > >> >> >>> > >> > doing the comparison. I am hacking this out super quick
> > so
> > >> >> please
> > >> >> >>> > >> forgive
> > >> >> >>> > >> > me:
> > >> >> >>> > >> >
> > >> >> >>> > >> > from itertools import izip
> > >> >> >>> > >> >
> > >> >> >>> > >> > with tb.openFile(...) as f:
> > >> >> >>> > >> > data = f.root.data
> > >> >> >>> > >> > data_i = iter(data)
> > >> >> >>> > >> > data_j = iter(data)
> > >> >> >>> > >> > data_i.next() # throw the first value away
> > >> >> >>> > >> > for i, j in izip(data_i, data_j):
> > >> >> >>> > >> > compare(i, j)
> > >> >> >>> > >> >
> > >> >> >>> > >> > You get the idea ;)
> > >> >> >>> > >> >
> > >> >> >>> > >> > Be Well
> > >> >> >>> > >> > Anthony
> > >> >> >>> > >> >
> > >> >> >>> > >> > 1. https://github.com/PyTables/PyTables/issues/27
> > >> >> >>> > >> >
> > >> >> >>> > >> >
> > >> >> >>> > >> > On Thu, Jan 3, 2013 at 9:25 AM, David Reed <
> > >> >> >>> dav...@gm...>
> > >> >> >>> > >> wrote:
> > >> >> >>> > >> >
> > >> >> >>> > >> >> I was hoping someone could help me out here.
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> This is from a post I put up on StackOverflow,
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> I am have a fairly large dataset that I store in HDF5
> and
> > >> >> access
> > >> >> >>> > using
> > >> >> >>> > >> >> PyTables. One operation I need to do on this dataset
> are
> > >> >> pairwise
> > >> >> >>> > >> >> comparisons between each of the elements. This
> requires 2
> > >> >> loops,
> > >> >> >>> one
> > >> >> >>> > to
> > >> >> >>> > >> >> iterate over each element, and an inner loop to iterate
> > >> over
> > >> >> >>> every
> > >> >> >>> > >> other
> > >> >> >>> > >> >> element. This operation thus looks at N(N-1)/2
> > comparisons.
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> For fairly small sets I found it to be faster to dump
> the
> > >> >> >>> contents
> > >> >> >>> > >> into a
> > >> >> >>> > >> >> multdimensional numpy array and then do my iteration. I
> > run
> > >> >> into
> > >> >> >>> > >> problems
> > >> >> >>> > >> >> with large sets because of memory issues and need to
> > access
> > >> >> each
> > >> >> >>> > >> element of
> > >> >> >>> > >> >> the dataset at run time.
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> Putting the elements into an array gives me about 600
> > >> >> >>> comparisons per
> > >> >> >>> > >> >> second, while operating on hdf5 data itself gives me
> > about
> > >> 300
> > >> >> >>> > >> comparisons
> > >> >> >>> > >> >> per second.
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> Is there a way to speed this process up?
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> Example follows (this is not my real code, just an
> > >> example):
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> *Small Set*:
> > >> >> >>> > >> >>
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> with tb.openFile(h5_file, 'r') as f:
> > >> >> >>> > >> >> data = f.root.data
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> N_elements = len(data)
> > >> >> >>> > >> >> elements = np.empty((N_irises, 1e5))
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> for ii, d in enumerate(data):
> > >> >> >>> > >> >> elements[ii] = data['element']
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> D = np.empty((N_irises, N_irises)) for ii in
> > >> >> xrange(N_elements):
> > >> >> >>> > >> >> for jj in xrange(ii+1, N_elements):
> > >> >> >>> > >> >> D[ii, jj] = compare(elements[ii], elements[jj])
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> *Large Set*:
> > >> >> >>> > >> >>
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> with tb.openFile(h5_file, 'r') as f:
> > >> >> >>> > >> >> data = f.root.data
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> N_elements = len(data)
> > >> >> >>> > >> >>
> > >> >> >>> > >> >> D = np.empty((N_irises, N_irises))
> > >> >> >>> > >> >> for ii in xrange(N_elements):
> > >> >> >>> > >> >> for jj in xrange(ii+1, N_elements):
> > >> >> >>> > >> >> D[ii, jj] = compare(data['element'][ii],
> > >> >> >>> > >> data['element'][jj])
> > >> >> >>> > >> >>
> > >> >> >>> > >> >>
> > >> >> >>> > >> >>
> > >> >> >>> > >> >>
> > >> >> >>> > >>
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >> >>> > >> >> Master Visual Studio, SharePoint, SQL, ASP.NET, C#
> 2012,
> > >> >> HTML5,
> > >> >> >>> CSS,
> > >> >> >>> > >> >> MVC, Windows 8 Apps, JavaScript and much more. Keep
> your
> > >> >> skills
> > >> >> >>> > current
> > >> >> >>> > >> >> with LearnDevNow - 3,200 step-by-step video tutorials
> by
> > >> >> >>> Microsoft
> > >> >> >>> > >> >> MVPs and experts. ON SALE this month only -- learn more
> > at:
> > >> >> >>> > >> >> http://p.sf.net/sfu/learnmore_122712
> > >> >> >>> > >> >> _______________________________________________
> > >> >> >>> > >> >> Pytables-users mailing list
> > >> >> >>> > >> >> Pyt...@li...
> > >> >> >>> > >> >>
> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >> >>
> > >> >> >>> > >> >>
> > >> >> >>> > >> >
> > >> >> >>> > >> >
> > >> >> >>> > >> >
> > >> >> >>> > >>
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >> >>> > >> > Master Visual Studio, SharePoint, SQL, ASP.NET, C#
> 2012,
> > >> >> HTML5,
> > >> >> >>> CSS,
> > >> >> >>> > >> > MVC, Windows 8 Apps, JavaScript and much more. Keep your
> > >> skills
> > >> >> >>> > current
> > >> >> >>> > >> > with LearnDevNow - 3,200 step-by-step video tutorials by
> > >> >> Microsoft
> > >> >> >>> > >> > MVPs and experts. ON SALE this month only -- learn more
> > at:
> > >> >> >>> > >> > http://p.sf.net/sfu/learnmore_122712
> > >> >> >>> > >> > _______________________________________________
> > >> >> >>> > >> > Pytables-users mailing list
> > >> >> >>> > >> > Pyt...@li...
> > >> >> >>> > >> >
> > https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >> >
> > >> >> >>> > >> >
> > >> >> >>> > >> -------------- next part --------------
> > >> >> >>> > >> An HTML attachment was scrubbed...
> > >> >> >>> > >>
> > >> >> >>> > >> ------------------------------
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >> >>> > >> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012,
> > >> HTML5,
> > >> >> >>> CSS,
> > >> >> >>> > >> MVC, Windows 8 Apps, JavaScript and much more. Keep your
> > >> skills
> > >> >> >>> current
> > >> >> >>> > >> with LearnDevNow - 3,200 step-by-step video tutorials by
> > >> >> Microsoft
> > >> >> >>> > >> MVPs and experts. ON SALE this month only -- learn more
> at:
> > >> >> >>> > >> http://p.sf.net/sfu/learnmore_122712
> > >> >> >>> > >>
> > >> >> >>> > >> ------------------------------
> > >> >> >>> > >>
> > >> >> >>> > >> _______________________________________________
> > >> >> >>> > >> Pytables-users mailing list
> > >> >> >>> > >> Pyt...@li...
> > >> >> >>> > >>
> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >> End of Pytables-users Digest, Vol 80, Issue 3
> > >> >> >>> > >> *********************************************
> > >> >> >>> > >>
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >> >>> > > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012,
> > >> HTML5,
> > >> >> CSS,
> > >> >> >>> > > MVC, Windows 8 Apps, JavaScript and much more. Keep your
> > skills
> > >> >> >>> current
> > >> >> >>> > > with LearnDevNow - 3,200 step-by-step video tutorials by
> > >> Microsoft
> > >> >> >>> > > MVPs and experts. ON SALE this month only -- learn more at:
> > >> >> >>> > > http://p.sf.net/sfu/learnmore_122712
> > >> >> >>> > > _______________________________________________
> > >> >> >>> > > Pytables-users mailing list
> > >> >> >>> > > Pyt...@li...
> > >> >> >>> > >
> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > -------------- next part --------------
> > >> >> >>> > An HTML attachment was scrubbed...
> > >> >> >>> >
> > >> >> >>> > ------------------------------
> > >> >> >>> >
> > >> >> >>> > Message: 2
> > >> >> >>> > Date: Thu, 3 Jan 2013 17:30:59 -0600
> > >> >> >>> > From: Anthony Scopatz <sc...@gm...>
> > >> >> >>> > Subject: Re: [Pytables-users] Pytables-users Digest, Vol 80,
> > >> Issue 4
> > >> >> >>> > To: Discussion list for PyTables
> > >> >> >>> > <pyt...@li...>
> > >> >> >>> > Message-ID:
> > >> >> >>> > <
> > >> >> >>> >
> > >> CAP...@ma...>
> > >> >> >>> > Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> >
> > >> >> >>> > Josh is right that you can just edit the code by hand (which
> > >> works
> > >> >> but
> > >> >> >>> > sucks).
> > >> >> >>> >
> > >> >> >>> > However, on Windows -- on the rare occasion when I also have
> to
> > >> >> >>> develop on
> > >> >> >>> > it -- I typically use a distribution that includes a
> compiler,
> > >> >> cython,
> > >> >> >>> > hdf5, and pytables already and then I install my development
> > >> version
> > >> >> >>> from
> > >> >> >>> > github OVER this. I recommend either EPD or Anaconda, though
> > >> other
> > >> >> >>> > distributions listed here [1] might also work.
> > >> >> >>> >
> > >> >> >>> > Be well
> > >> >> >>> > Anthony
> > >> >> >>> >
> > >> >> >>> > 1. http://numfocus.org/projects-2/software-distributions/
> > >> >> >>> >
> > >> >> >>> >
> > >> >> >>> > On Thu, Jan 3, 2013 at 3:46 PM, Josh Ayers <
> > jos...@gm...
> > >> >
> > >> >> >>> wrote:
> > >> >> >>> >
> > >> >> >>> > > The change was in pure Python code, so you should be able
> to
> > >> just
> > >> >> >>> paste
> > >> >> >>> > in
> > >> >> >>> > > the changes to your local copy. Start with the
> > >> >> table.Column.__iter__
> > >> >> >>> > > method (lines 3296-3310) here.
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> https://github.com/PyTables/PyTables/blob/b479ed025f4636f7f4744ac83a89bc947808907c/tables/table.py
> > >> >> >>> > >
> > >> >> >>> > > It needs to be modified slightly because it uses some
> > >> additional
> > >> >> >>> features
> > >> >> >>> > > that aren't available in the released version (the
> > >> out=buf_slice
> > >> >> >>> argument
> > >> >> >>> > > to table.read). The following should work.
> > >> >> >>> > >
> > >> >> >>> > > def __iter__(self):
> > >> >> >>> > > table = self.table
> > >> >> >>> > > itemsize = self.dtype.itemsize
> > >> >> >>> > > nrowsinbuf = table._v_file.params['IO_BUFFER_SIZE']
> > //
> > >> >> >>> itemsize
> > >> >> >>> > > max_row = len(self)
> > >> >> >>> > > for start_row in xrange(0, len(self), nrowsinbuf):
> > >> >> >>> > > end_row = min([start_row + nrowsinbuf,
> max_row])
> > >> >> >>> > > buf = table.read(start_row, end_row, 1,
> > >> >> >>> field=self.pathname)
> > >> >> >>> > > for row in buf:
> > >> >> >>> > > yield row
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > > I haven't tested this, but I think it will work.
> > >> >> >>> > >
> > >> >> >>> > > Josh
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > >
> > >> >> >>> > > On Thu, Jan 3, 2013 at 1:25 PM, David Reed <
> > >> >> dav...@gm...>
> > >> >> >>> > wrote:
> > >> >> >>> > >
> > >> >> >>> > >> I apologize if I'm starting to sound helpless, but I'm
> > forced
> > >> to
> > >> >> >>> work on
> > >> >> >>> > >> Windows 7 at work and have never had luck compiling python
> > >> source
> > >> >> >>> > >> successfully. I have had to rely on precompiled binaries
> > and
> > >> now
> > >> >> >>> its
> > >> >> >>> > >> biting me in the butt.
> > >> >> >>> > >>
> > >> >> >>> > >> Is there any quick fix I can do to improve this iteration
> > >> using
> > >> >> >>> v2.4.0?
> > >> >> >>> > >>
> > >> >> >>> > >>
> > >> >> >>> > >> On Thu, Jan 3, 2013 at 3:17 PM, <
> > >> >> >>> > >> pyt...@li...> wrote:
> > >> >> >>> > >>
> > >> >> >>> > >>> Send Pytables-users mailing list submissions to
> > >> >> >>> > >>> pyt...@li...
> > >> >> >>> > >>>
> > >> >> >>> > >>> To subscribe or unsubscribe via the World Wide Web, visit
> > >> >> >>> > >>>
> > >> >> >>> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >>> or, via email, send a message with subject or body 'help'
> > to
> > >> >> >>> > >>> pyt...@li...
> > >> >> >>> > >>>
> > >> >> >>> > >>> You can reach the person managing the list at
> > >> >> >>> > >>> pyt...@li...
> > >> >> >>> > >>>
> > >> >> >>> > >>> When replying, please edit your Subject line so it is
> more
> > >> >> specific
> > >> >> >>> > >>> than "Re: Contents of Pytables-users digest..."
> > >> >> >>> > >>>
> > >> >> >>> > >>>
> > >> >> >>> > >>> Today's Topics:
> > >> >> >>> > >>>
> > >> >> >>> > >>> 1. Re: Pytables-users Digest, Vol 80, Issue 2 (David
> > Reed)
> > >> >> >>> > >>> 2. Re: Pytables-users Digest, Vol 80, Issue 3 (David
> > Reed)
> > >> >> >>> > >>>
> > >> >> >>> > >>>
> > >> >> >>> > >>>
> > >> >> >>>
> > >> ----------------------------------------------------------------------
> > >> >> >>> > >>>
> > >> >> >>> > >>> Message: 1
> > >> >> >>> > >>> Date: Thu, 3 Jan 2013 13:44:29 -0500
> > >> >> >>> > >>> From: David Reed <dav...@gm...>
> > >> >> >>> > >>> Subject: Re: [Pytables-users] Pytables-users Digest, Vol
> > 80,
> > >> >> Issue
> > >> >> >>> 2
> > >> >> >>> > >>> To: pyt...@li...
> > >> >> >>> > >>> Message-ID:
> > >> >> >>> > >>> <CAM6XA7=8ocg5WPD4KLSvLhSw-3BCvq5u7MRxq3Ajd6ha=
> > >> >> >>> > >>> ev...@ma...>
> > >> >> >>> > >>> Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> > >>>
> > >> >> >>> > >>> Thanks Anthony, but unless Im missing something I don't
> > think
> > >> >> that
> > >> >> >>> > method
> > >> >> >>> > >>> will work since this will only be comparing the ith
> element
> > >> with
> > >> >> >>> ith+1
> > >> >> >>> > >>> element. I still need 2 for loops right?
> > >> >> >>> > >>>
> > >> >> >>> > >>> Using itertools might speed things up though, I've never
> > used
> > >> >> them
> > >> >> >>> so I
> > >> >> >>> > >>> will give it a shot and let you know how it goes. Looks
> > >> like I
> > >> >> >>> need to
> > >> >> >>> > >>> download the latest release before I do that too. Thanks
> > for
> > >> >> the
> > >> >> >>> help.
> > >> >> >>> > >>>
> > >> >> >>> > >>> -Dave
> > >> >> >>> > >>>
> > >> >> >>> > >>>
> > >> >> >>> > >>>
> > >> >> >>> > >>> On Thu, Jan 3, 2013 at 12:12 PM, <
> > >> >> >>> > >>> pyt...@li...> wrote:
> > >> >> >>> > >>>
> > >> >> >>> > >>> > Send Pytables-users mailing list submissions to
> > >> >> >>> > >>> > pyt...@li...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > To subscribe or unsubscribe via the World Wide Web,
> visit
> > >> >> >>> > >>> >
> > >> >> >>> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >>> > or, via email, send a message with subject or body
> 'help'
> > >> to
> > >> >> >>> > >>> > pyt...@li...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > You can reach the person managing the list at
> > >> >> >>> > >>> > pyt...@li...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > When replying, please edit your Subject line so it is
> > more
> > >> >> >>> specific
> > >> >> >>> > >>> > than "Re: Contents of Pytables-users digest..."
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Today's Topics:
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > 1. Re: Nested Iteration of HDF5 using PyTables
> > (Anthony
> > >> >> >>> Scopatz)
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> >
> > >> >>
> > ----------------------------------------------------------------------
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Message: 1
> > >> >> >>> > >>> > Date: Thu, 3 Jan 2013 11:11:47 -0600
> > >> >> >>> > >>> > From: Anthony Scopatz <sc...@gm...>
> > >> >> >>> > >>> > Subject: Re: [Pytables-users] Nested Iteration of HDF5
> > >> using
> > >> >> >>> PyTables
> > >> >> >>> > >>> > To: Discussion list for PyTables
> > >> >> >>> > >>> > <pyt...@li...>
> > >> >> >>> > >>> > Message-ID:
> > >> >> >>> > >>> > <CAPk-6T5b=
> > >> >> >>> > >>> >
> 1EG...@ma...
> > >
> > >> >> >>> > >>> > Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > HI David,
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Tables and table column iteration have been overhauled
> > >> fairly
> > >> >> >>> > recently
> > >> >> >>> > >>> [1].
> > >> >> >>> > >>> > So you might try creating two iterators, offset by
> one,
> > >> and
> > >> >> then
> > >> >> >>> > >>> doing the
> > >> >> >>> > >>> > comparison. I am hacking this out super quick so
> please
> > >> >> forgive
> > >> >> >>> me:
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > from itertools import izip
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > with tb.openFile(...) as f:
> > >> >> >>> > >>> > data = f.root.data
> > >> >> >>> > >>> > data_i = iter(data)
> > >> >> >>> > >>> > data_j = iter(data)
> > >> >> >>> > >>> > data_i.next() # throw the first value away
> > >> >> >>> > >>> > for i, j in izip(data_i, data_j):
> > >> >> >>> > >>> > compare(i, j)
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > You get the idea ;)
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Be Well
> > >> >> >>> > >>> > Anthony
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > 1. https://github.com/PyTables/PyTables/issues/27
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > On Thu, Jan 3, 2013 at 9:25 AM, David Reed <
> > >> >> >>> dav...@gm...>
> > >> >> >>> > >>> wrote:
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > > I was hoping someone could help me out here.
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > This is from a post I put up on StackOverflow,
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > I am have a fairly large dataset that I store in HDF5
> > and
> > >> >> >>> access
> > >> >> >>> > >>> using
> > >> >> >>> > >>> > > PyTables. One operation I need to do on this dataset
> > are
> > >> >> >>> pairwise
> > >> >> >>> > >>> > > comparisons between each of the elements. This
> > requires 2
> > >> >> >>> loops,
> > >> >> >>> > one
> > >> >> >>> > >>> to
> > >> >> >>> > >>> > > iterate over each element, and an inner loop to
> iterate
> > >> over
> > >> >> >>> every
> > >> >> >>> > >>> other
> > >> >> >>> > >>> > > element. This operation thus looks at N(N-1)/2
> > >> comparisons.
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > For fairly small sets I found it to be faster to dump
> > the
> > >> >> >>> contents
> > >> >> >>> > >>> into a
> > >> >> >>> > >>> > > multdimensional numpy array and then do my
> iteration. I
> > >> run
> > >> >> >>> into
> > >> >> >>> > >>> problems
> > >> >> >>> > >>> > > with large sets because of memory issues and need to
> > >> access
> > >> >> >>> each
> > >> >> >>> > >>> element
> > >> >> >>> > >>> > of
> > >> >> >>> > >>> > > the dataset at run time.
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > Putting the elements into an array gives me about 600
> > >> >> >>> comparisons
> > >> >> >>> > per
> > >> >> >>> > >>> > > second, while operating on hdf5 data itself gives me
> > >> about
> > >> >> 300
> > >> >> >>> > >>> > comparisons
> > >> >> >>> > >>> > > per second.
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > Is there a way to speed this process up?
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > Example follows (this is not my real code, just an
> > >> example):
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > *Small Set*:
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > with tb.openFile(h5_file, 'r') as f:
> > >> >> >>> > >>> > > data = f.root.data
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > N_elements = len(data)
> > >> >> >>> > >>> > > elements = np.empty((N_irises, 1e5))
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > for ii, d in enumerate(data):
> > >> >> >>> > >>> > > elements[ii] = data['element']
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > D = np.empty((N_irises, N_irises)) for ii in
> > >> >> >>> xrange(N_elements):
> > >> >> >>> > >>> > > for jj in xrange(ii+1, N_elements):
> > >> >> >>> > >>> > > D[ii, jj] = compare(elements[ii],
> elements[jj])
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > *Large Set*:
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > with tb.openFile(h5_file, 'r') as f:
> > >> >> >>> > >>> > > data = f.root.data
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > N_elements = len(data)
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > D = np.empty((N_irises, N_irises))
> > >> >> >>> > >>> > > for ii in xrange(N_elements):
> > >> >> >>> > >>> > > for jj in xrange(ii+1, N_elements):
> > >> >> >>> > >>> > > D[ii, jj] = compare(data['element'][ii],
> > >> >> >>> > >>> > data['element'][jj])
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> >
> > >> >> >>> > >>>
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >> >>> > >>> > > Master Visual Studio, SharePoint, SQL, ASP.NET, C#
> > 2012,
> > >> >> >>> HTML5,
> > >> >> >>> > CSS,
> > >> >> >>> > >>> > > MVC, Windows 8 Apps, JavaScript and much more. Keep
> > your
> > >> >> skills
> > >> >> >>> > >>> current
> > >> >> >>> > >>> > > with LearnDevNow - 3,200 step-by-step video tutorials
> > by
> > >> >> >>> Microsoft
> > >> >> >>> > >>> > > MVPs and experts. ON SALE this month only -- learn
> more
> > >> at:
> > >> >> >>> > >>> > > http://p.sf.net/sfu/learnmore_122712
> > >> >> >>> > >>> > > _______________________________________________
> > >> >> >>> > >>> > > Pytables-users mailing list
> > >> >> >>> > >>> > > Pyt...@li...
> > >> >> >>> > >>> > >
> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > -------------- next part --------------
> > >> >> >>> > >>> > An HTML attachment was scrubbed...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > ------------------------------
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>>
> > >> >> >>> >
> > >> >> >>>
> > >> >>
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >> >>> > >>> > Master Visual Studio, SharePoint, SQL, ASP.NET, C#
> 2012,
> > >> >> HTML5,
> > >> >> >>> CSS,
> > >> >> >>> > >>> > MVC, Windows 8 Apps, JavaScript and much more. Keep
> your
> > >> >> skills
> > >> >> >>> > current
> > >> >> >>> > >>> > with LearnDevNow - 3,200 step-by-step video tutorials
> by
> > >> >> >>> Microsoft
> > >> >> >>> > >>> > MVPs and experts. ON SALE this month only -- learn more
> > at:
> > >> >> >>> > >>> > http://p.sf.net/sfu/learnmore_122712
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > ------------------------------
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > _______________________________________________
> > >> >> >>> > >>> > Pytables-users mailing list
> > >> >> >>> > >>> > Pyt...@li...
> > >> >> >>> > >>> >
> > >> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > End of Pytables-users Digest, Vol 80, Issue 2
> > >> >> >>> > >>> > *********************************************
> > >> >> >>> > >>> >
> > >> >> >>> > >>> -------------- next part --------------
> > >> >> >>> > >>> An HTML attachment was scrubbed...
> > >> >> >>> > >>>
> > >> >> >>> > >>> ------------------------------
> > >> >> >>> > >>>
> > >> >> >>> > >>> Message: 2
> > >> >> >>> > >>> Date: Thu, 3 Jan 2013 15:17:01 -0500
> > >> >> >>> > >>> From: David Reed <dav...@gm...>
> > >> >> >>> > >>> Subject: Re: [Pytables-users] Pytables-users Digest, Vol
> > 80,
> > >> >> Issue
> > >> >> >>> 3
> > >> >> >>> > >>> To: pyt...@li...
> > >> >> >>> > >>> Message-ID:
> > >> >> >>> > >>> <
> > >> >> >>> > >>>
> > >> >> CAM...@ma...
> > >> >> >>> >
> > >> >> >>> > >>> Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> > >>>
> > >> >> >>> > >>> Thanks a lot for the help so far guys!
> > >> >> >>> > >>>
> > >> >> >>> > >>> Looking at itertools, I found what I believe to be the
> > >> perfect
> > >> >> >>> function
> > >> >> >>> > >>> for
> > >> >> >>> > >>> what I need, itertools.combinations. This appears to be a
> > >> valid
> > >> >> >>> > >>> replacement
> > >> >> >>> > >>> to the method proposed.
> > >> >> >>> > >>>
> > >> >> >>> > >>> There is a small problem that I didn't mention is that my
> > >> >> compare
> > >> >> >>> > >>> function
> > >> >> >>> > >>> actually takes as inputs 2 columns from the table. Like
> so:
> > >> >> >>> > >>>
> > >> >> >>> > >>> D = np.empty((N_irises, N_irises))
> > >> >> >>> > >>> for ii in xrange(N_elements):
> > >> >> >>> > >>> for jj in xrange(ii+1, N_elements):
> > >> >> >>> > >>> D[ii, jj] = compare(data['element1'][ii],
> > >> >> >>> > >>> data['element1'][jj],data['element2'][ii],
> > >> >> >>> > >>> data['element2'][jj])
> > >> >> >>> > >>>
> > >> >> >>> > >>> Is there an efficient way of using itertools with this
> > >> >> structure?
> > >> >> >>> > >>>
> > >> >> >>> > >>>
> > >> >> >>> > >>> On Thu, Jan 3, 2013 at 1:29 PM, <
> > >> >> >>> > >>> pyt...@li...> wrote:
> > >> >> >>> > >>>
> > >> >> >>> > >>> > Send Pytables-users mailing list submissions to
> > >> >> >>> > >>> > pyt...@li...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > To subscribe or unsubscribe via the World Wide Web,
> visit
> > >> >> >>> > >>> >
> > >> >> >>> https://lists.sourceforge.net/lists/listinfo/pytables-users
> > >> >> >>> > >>> > or, via email, send a message with subject or body
> 'help'
> > >> to
> > >> >> >>> > >>> > pyt...@li...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > You can reach the person managing the list at
> > >> >> >>> > >>> > pyt...@li...
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > When replying, please edit your Subject line so it is
> > more
> > >> >> >>> specific
> > >> >> >>> > >>> > than "Re: Contents of Pytables-users digest..."
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Today's Topics:
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > 1. Re: Nested Iteration of HDF5 using PyTables (Josh
> > >> Ayers)
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> >
> > >> >>
> > ----------------------------------------------------------------------
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Message: 1
> > >> >> >>> > >>> > Date: Thu, 3 Jan 2013 10:29:33 -0800
> > >> >> >>> > >>> > From: Josh Ayers <jos...@gm...>
> > >> >> >>> > >>> > Subject: Re: [Pytables-users] Nested Iteration of HDF5
> > >> using
> > >> >> >>> PyTables
> > >> >> >>> > >>> > To: Discussion list for PyTables
> > >> >> >>> > >>> > <pyt...@li...>
> > >> >> >>> > >>> > Message-ID:
> > >> >> >>> > >>> > <
> > >> >> >>> > >>> >
> > >> >> >>>
> > CAC...@ma...
> > >> >
> > >> >> >>> > >>> > Content-Type: text/plain; charset="iso-8859-1"
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > David,
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > The change in issue 27 was only for iteration over a
> > >> >> >>> tables.Column
> > >> >> >>> > >>> > instance. To use it, tweak Anthony's code as follows.
> > >> This
> > >> >> will
> > >> >> >>> > >>> iterate
> > >> >> >>> > >>> > over the "element" column, as in your original example.
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Note also that this will only work with the development
> > >> >> version
> > >> >> >>> of
> > >> >> >>> > >>> PyTables
> > >> >> >>> > >>> > available on github. It will be very slow using the
> > >> released
> > >> >> >>> v2.4.0.
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > from itertools import izip
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > with tb.openFile(...) as f:
> > >> >> >>> > >>> > data = f.root.data.cols.element
> > >> >> >>> > >>> > data_i = iter(data)
> > >> >> >>> > >>> > data_j = iter(data)
> > >> >> >>> > >>> > data_i.next() # throw the first value away
> > >> >> >>> > >>> > for i, j in izip(data_i, data_j):
> > >> >> >>> > >>> > compare(i, j)
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > Hope that helps,
> > >> >> >>> > >>> > Josh
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > On Thu, Jan 3, 2013 at 9:11 AM, Anthony Scopatz <
> > >> >> >>> sc...@gm...>
> > >> >> >>> > >>> wrote:
> > >> >> >>> > >>> >
> > >> >> >>> > >>> > > HI David,
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > Tables and table column iteration have been
> overhauled
> > >> >> fairly
> > >> >> >>> > >>> recently
> > >> >> >>> > >>> > > [1]. So you might try creating two iterators, offset
> > by
> > >> >> one,
> > >> >> >>> and
> > >> >> >>> > >>> then
> > >> >> >>> > >>> > > doing the comparison. I am hacking this out super
> > quick
> > >> so
> > >> >> >>> please
> > >> >> >>> > >>> > forgive
> > >> >> >>> > >>> > > me:
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > from itertools import izip
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > with tb.openFile(...) as f:
> > >> >> >>> > >>> > > data = f.root.data
> > >> >> >>> > >>> > > data_i = iter(data)
> > >> >> >>> > >>> > > data_j = iter(data)
> > >> >> >>> > >>> > > data_i.next() # throw the first value away
> > >> >> >>> > >>> > > for i, j in izip(data_i, data_j):
> > >> >> >>> > >>> > > compare(i, j)
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > You get the idea ;)
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > Be Well
> > >> >> >>> > >>> > > Anthony
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > 1. https://github.com/PyTables/PyTables/issues/27
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > > On Thu, Jan 3, 2013 at 9:25 AM, David Reed <
> > >> >> >>> dav...@gm...
> > >> >> >>> > >
> > >> >> >>> > >>> > wrote:
> > >> >> >>> > >>> > >
> > >> >> >>> > >>> > >> I was hoping someone could help me out here.
> > >> >> >>> > >>> > >>
> > >> >> >>> > >>> > >> This is from a post I put up on StackOverflow,
> > >> >> >>> > >>> > >>
> > >> >> >>> > >>> > >> I am have a fairly large dataset that I store in
> HDF5
> > >> and
> > >> >> >>> access
> > >> >> >>> > >>> using
> > >> >> >>> > >>> > >> PyTables. One operation I need to do on this dataset
> > are
> > >> >> >>> pairwise
> > >> >> >>> > >>> > >> comparisons between each of the elements. This
> > requires
> > >> 2
> > >> >> >>> loops,
> > >> >> >>> > >>> one to
> > >> >> >>> > >>> > >> iterate over each element, and an inner loop to
> > iterate
> > >> >> over
> > >> >> >>> every
> > >> >> >>> > >>> other
> > >> >> >>> > >>> > >> element. This operation thus looks at N(N-1)/2
> > >> comparisons.
> > >> >> >>> > >>> > >>
> > >> >> >>> > >>> > >> For fairly small sets I found it to be faster to
> dump
> > >> the
> > >> >> >>> contents
> > >> >> >>> > >>> into
> > >> >> >>> > >>> > a
> > >> >> >>> > >>> > >> multdimensional numpy array and then do my
> iteration.
> > I
> > >> run
> > >> >> >>> into
> > >> >> >>> > >>> > problems
> > >> >> >>> > >>> > >> with large sets because of memory issues and need to
> > >> access
> > >> >> >>> each
> > >> >> >>> > >>> > element of
> > >> >> >>> > >>> > >> the dataset at run time.
> > >> >> >>> > >>> > >>
> > >> >> >>> > >>> > >> Putting the elements into an array gives me ...
[truncated message content] |
