Mailman 3 October 2003 - SciPy-Dev

problems with latest cvs
by Nils Wagner Oct. 27, 2003

Oct. 27, 2003

Dear experts, A build from latest cvs failed Traceback (most recent call last): File "setup.py", line 163, in ? setup_package(ignore_packages) File "setup.py", line 153, in setup_package url = "http://www.scipy.org", File "scipy_core/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/usr/lib/python2.3/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/lib/python2.3/distutils/dist.py", line 907, in run_commands self.run_command(cmd) File "/usr/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() File "/usr/lib/python2.3/distutils/command/build.py", line 107, in run self.run_command(cmd_name) File "/usr/lib/python2.3/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib/python2.3/distutils/dist.py", line 927, in run_command cmd_obj.run() File "scipy_core/scipy_distutils/command/run_f2py.py", line 70, in run ext.sources = self.f2py_sources(ext.sources,ext) File "scipy_core/scipy_distutils/command/run_f2py.py", line 118, in f2py_sources (base, source_ext) = os.path.splitext(source) File "/usr/lib/python2.3/posixpath.py", line 92, in splitext i = p.rfind('.') AttributeError: SourceFilter instance has no attribute 'rfind' Nils

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Patch for pilutils
by Fernando Perez Oct. 24, 2003

Oct. 24, 2003

Hi all, here's a simple patch for pilutil which adds a simple 'flatten' option to the image reading functions imread. Here are the resulting definition and docstrings: In [2]: scipy.fromimage? Definition: scipy.fromimage(im, flatten=0) Docstring: Takes a PIL image and returns a copy of the image in a Numeric container. If the image is RGB returns a 3-dimensional array: arr[:,:,n] is each channel Optional arguments: - flatten (0): if true, the image is flattened by calling convert('F') on the image object before extracting the numerical data. This flattens the color layers into a single grayscale layer. Note that the supplied image object is NOT modified. In [3]: scipy.imread? Definition: scipy.imread(name, flatten=0) Docstring: Read an image file from a filename. Optional arguments: - flatten (0): if true, the image is flattened by calling convert('F') on the resulting image object. This flattens the color layers into a single grayscale layer. This is useful in case you want to load straight from an image file (jpeg, tiff, ...) but you want a single grayscale array to do numerics on. The change is fully backwards compatible. I did it because we needed here to easily read images for testing some numerical transformations without dealing with the color channels. It was easier to patch scipy than to tell my coworkers to remember to convert every image first :) Comments? I think I can commit to CVS, but I don't want to without some feedback first on whether people like/dislike the idea. Especially because it's not a bugfix, it's a new feature (albeit a small one). Regards, Fernando. ps. Hey Travis, thanks for committing the weave.catalog fix. I was going to include that today in the patch and I checked the CVS, to find you'd done it. diff -aur old/scipy/pilutil.py new/scipy/pilutil.py --- old/scipy/pilutil.py 2003-10-24 12:09:18.000000000 -0600 +++ new/scipy/pilutil.py 2003-10-24 11:57:00.000000000 -0600 @@ -29,11 +29,17 @@ return bytedata + cast[_UInt8](low) -def imread(name): - """Read an image file. +def imread(name,flatten=0): + """Read an image file from a filename. + + Optional arguments: + + - flatten (0): if true, the image is flattened by calling convert('F') on + the resulting image object. This flattens the color layers into a single + grayscale layer. """ im = Image.open(name) - return fromimage(im) + return fromimage(im,flatten=flatten) def imsave(name, arr): """Save an array to an image file. @@ -42,11 +48,20 @@ im.save(name) return -def fromimage(im): +def fromimage(im,flatten=0): """Takes a PIL image and returns a copy of the image in a Numeric container. If the image is RGB returns a 3-dimensional array: arr[:,:,n] is each channel - """ + + Optional arguments: + + - flatten (0): if true, the image is flattened by calling convert('F') on + the image object before extracting the numerical data. This flattens the + color layers into a single grayscale layer. Note that the supplied image + object is NOT modified.""" + assert Image.isImageType(im), "Not a PIL image." + if flatten: + im = im.convert('F') mode = im.mode adjust = 0 if mode == '1':

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building RPMs
by Anthony Joseph Seward Oct. 21, 2003

Oct. 21, 2003

I'm trying to streamline and simplify the building of my SciPy RPMs. It would greatly help if the MANIFEST.in and setup.cfg files that I've attached are included in the scipy_core/scipy_distutils directory. Comments? Tony -- Anthony Joseph Seward <anthony.seward(a)ieee.org>

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Found fix for a long-standing bug in weave.catalog
by Fernando Perez Oct. 17, 2003

Oct. 17, 2003

Hi all, on and off I've been seeing very strange behavior from weave.inline(). Basically it would rebuild functions which it had already seen before, in a rather erratic manner. Today I finally dove in to try and fix, and after a _lot_ of print statements all over weave, I think I got it. In catalog.py, the add_function_persistent() method NEEDS as its final line: cat.close() This closes the shelve catalog object, which guarantees that the changes are actually committed to disk. From the shelve docs: Dependent on the implementation, closing a persistent dictionary may or may not be necessary to flush changes to disk. It's quite possible that others haven't seen this because they are on different platforms, or stress weave in different ways. I've actually beeen using inline() for a long time, and only with one particular library I have, do I see this problem. But when it hits you, it's extremely annoying, since you end up paying the compilation time overhead on _every_ function call. Kind of defeats the purpose of weave :) Eric, this is the bug I told you about at SciPy'03, which I was seeing on and off. Quite tricky to track down, but now that I had to understand most of how weave.inline() & friends work, my hat is off to you. That's one beautiful piece of code (messy, but amazing :) It would be great if someone could double check that this is ineed ok (I'm pretty sure it is) and apply that single line change to the sources. I tested it against my library, and now it behaves reliably as it should (which it neveer had before). Many thanks, Fernando.

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Added Matlab version 5.0 file reading support
by Travis Oliphant Oct. 16, 2003

Oct. 16, 2003

Thanks to the good start provided by Heinko, I have completed addition of read support for MATLAB(tm) version 5.0 mat files. Sparse matrices are also read and converted to SciPy sparse matrices if you have compiled the sparse package (turned off by default). The changes are in CVS and are part of the io.loadmat function (it now recognized v5 files). Matlab(tm) Structures and objects are handled as (arrays of) dummy classes and are also supported. Cell arrays are handled as an Object array. -Travis O.

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matFile module
by Heiko Henkelmann Oct. 15, 2003

Oct. 15, 2003

Dear All, due to popular demand on this list I'm giving you the chance to look at a module which I'm currently developing. I'm not done with it but I figured in terms of avoiding duplicated efforts it would be a good point to show it to you. It is a pure python implementation and enables users to read ML Version 5 compatible files. At this point it is able to read anything but sparse matrices. Not having looked at Nigel Wades matfile I can't tell you what the differences to my implementation are. Feedback, especially on cross platform compatibility and every kind of test results would be very welcome. Thanx Heiko

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io.loadmat
by Nils Wagner Oct. 14, 2003

Oct. 14, 2003

Dear experts, I need some advice concerning loadmat loadmat -- read a MATLAB (version <= 4) style mat file loadmat(name, dict=None, appendmat=1) Load the MATLAB mat file saved in level 1.0 format. If name is a full path name load it in. Otherwise search for the file on the sys.path list and load the first one found (the current directory is searched first). Only Level 1.0 MAT files are supported so far. Inputs: name -- name of the mat file (don't need .mat extension) dict -- the dictionary to insert into. If none the variables will be returned in a dictionary. appendmat -- non-zero to append the .mat extension to the end of the given filename. Outputs: If dict is None, then a dictionary of names and objects representing the stored arrays is returned. What is meaning of level 1.0 format ? Afaik, the current version of Matlab is 6.5. However loadmat seems to be restricted to version <=4. Is there any progress in upgrading this feature ? from scipy import * file=open("matrizen_red.mat",'r') io.loadmat(file,appendmat=0) raceback (most recent call last): File "matlab.py", line 3, in ? io.loadmat(file,appendmat=0) File "/usr/local/lib/python2.1/site-packages/scipy/io/mio.py", line 348, in loadmat if os.sep in name: TypeError: 'in' or 'not in' needs sequence right argument Any suggestion ? Nils

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gui_thread and chaco under Linux
by Pearu Peterson Oct. 10, 2003

Oct. 10, 2003

Hi, I have struggling with getting chaco to work under Linux. Currently the following happens: >>> import gui_thread >>> gui_thread.start() <Importing wxPython... done.> >>> >>> from chaco.wxplt import * Xlib: unexpected async reply (sequence 0x68)! After some research I found that the above failure occurs because wx functions are not called from the same thread that imported wxPython, first this happens in traits/wxtrait_sheet.py. When importing chaco.wxplt from the same thread that imported wxPython (by inserting `import chaco.wxplt` just after wxPython import in gui_thread/gui_thread_guts.py), then we have this: >>> import gui_thread >>> gui_thread.start() <Importing wxPython... done.> >>> >>> from chaco.wxplt import * >>> but now trying to make a simple plot fails with python hang: >>> plot([1,2]) Xlib: unexpected async reply (sequence 0x7a)! Again, the reason for this failure is that the above plot function was called from the main but wrong thread. For example, inserting also `chaco.wxplt.plot([1,2])` to gui_thread/gui_thread_guts.py will result a working wx plot window as well as working python prompt. This example worked because the plot function was called from the right (secondary) thread. While having chaco imports in gui_thread/gui_thread_guts.py can be acceptable but I have failed to figure out how to force calling plot function from the prompt (that runs under the main thread) so that it will be executed in the second thread (that imported wxPython and chaco). Somehow I am getting a feeling that the gui_thread concept is just not working under Linux (or any Unixes that run under X) because X is not thread safe and therefore there is a condition that wxPython must be imported and used strictly within the same thread. Please, correct me if I am wrong on this! The following solutions come into my head: 1) Introduce a wrapper around wxPython module that transforms all accesses to wxPython data from the main thread to the secondary thread (that imports wxPython). I think this can be achieved without touching chaco at all through similar hooks that are used in ppimport. 2) Import wxPython from the main thread and create an interactive prompt thread from wxPython app. This would require implementing a prompt very similar to PyCrust but that would have I/O from the terminal. Both solutions would require a lot of work and I would hope that there would be a simpler solution. For example, getting gui_thread to work correctly under X. Other thoughts? Regards, Pearu

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Saving plots
by Martin Kuemmel Oct. 7, 2003

Oct. 7, 2003

Hi everybody! I am working since a month now with python, and I have to say that I am impressed about its capabilities. Now I encountered a problem, and hope there will be a solution in scientific python. I have to make plots in a noninteractive way, and I have to store them in a html-compatible format like gif, or jpeg, or png or whatsever. The help of the plotting package says that plots can be saved, but the format is not specified. So, is the a way to get gif's, jpg'or similar?? Yours, Martin

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Scipy roundup anonymnous user behaves strangely
by Pearu Peterson Oct. 6, 2003

Oct. 6, 2003

Hi, During last weeks I have resolved several roundup issues and set them "resolved". However, I have noticed that some anonymous user is setting them "chatting" again and without adding any comments why it is doing so. So, would it be possible to discard those roundup issue editing attempts that leave "Change note" empty? Thanks, Pearu

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