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 372 </script>
 373 <title>PyPlotSuite README File</title>
 374 </head>
 375 <body>
 376 <div id="header">
 377 <h1>PyPlotSuite README File</h1>
 378 <div id="toc">
 379   <div id="toctitle">Table of Contents</div>
 380   <noscript><p><b>JavaScript must be enabled in your browser to display the table of contents.</b></p></noscript>
 381 </div>
 382 </div>
 383 <div id="preamble">
 384 <div class="sectionbody">
 385 <div class="sidebarblock">
 386 <div class="sidebar-content">
 387 <div class="sidebar-title">Copyright and License</div>
 388 <p>Copyright &#169; 2006-2007 Antonino Ingargiola &lt;tritemio@gmail.com&gt;</p>
 389 <p>This program is free software; you can redistribute it and/or modify
 390 it under the terms of the GNU General Public License as published by
 391 the Free Software Foundation; either version 2 of the License, or
 392 (at your option) any later version.</p>
 393 <p>This program is distributed in the hope that it will be useful,
 394 but WITHOUT ANY WARRANTY; without even the implied warranty of
 395 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 396 GNU General Public License for more details.</p>
 397 <p>For more information read the file LICENSE.txt in the source directory.</p>
 398 </div></div>
 399 </div>
 400 </div>
 401 <h2>Project Description</h2>
 402 <div class="sectionbody">
 403 <p><strong>PyPlotSuite</strong> is a set of graphical tools to quick visualize and explore/analyze
 404 monodimentional and bidimensional data. The plot created can be saved in a
 405 variety of image formats to produce publication quality graphs.</p>
 406 <p>At the moment the project is composed by two little stand alone applications:
 407 <strong>ImageAnalyzer</strong> and <strong>Plotfile2</strong>. ImageAnalyzer is focused towards images (or any
 408 2D data, such as arrays) visualization, analysis, and measurement. Plotfile2
 409 focus is towards simple data series visualization, with the possibility to
 410 quick modify many plot characteristics. Both applications can save the result
 411 on a multitude of image file formats (png, eps, jpeg, pdf, and more).</p>
 412 <p>PyPlotSuite is written in python, using the GTK gui toolkit (through the python
 413 binding pygtk, and using Glade-2 to layout the windows). All plots are created
 414 with the great Matplotlib python 2D graphic library. Matplotlib is such a good
 415 tool that the PyPlotSuite applications are only tiny wrapper around Matplotlib
 416 functionality. Also some Numpy functionality are used both through Matplotlib
 417 (which requires Numpy) and both directly.</p>
 418 <div class="hlist"><table>
 419 <tr>
 420 <td class="hlist1">
 421 Home Page
 422 </td>
 423 <td class="hlist2">
 424 <a href="http://pyplotsuite.sourceforge.net">http://pyplotsuite.sourceforge.net</a>
 425 </td>
 426 </tr>
 427 <tr>
 428 <td class="hlist1">
 429 <strong>Latest Version</strong>
 430 </td>
 431 <td class="hlist2">
 432 0.1-alpha8
 433 </td>
 434 </tr>
 435 </table></div>
 436 </div>
 437 <h2>NEWS</h2>
 438 <div class="sectionbody">
 439 <h3>0.1-alpha8</h3>
 440 <ul>
 441 <li>
 442 <p>
 443 Added multiplatform installer using distutils. Now to install the pyplotsuite
 444   system-wide just do "python setup.py install" form the source tree with
 445   administrative privileges.
 446 </p>
 447 </li>
 448 <li>
 449 <p>
 450 Various bug-fixes thanks to David Trémouilles' bug reports and patches (now
 451   the open dialog remebers the last dir).
 452 </p>
 453 </li>
 454 <li>
 455 <p>
 456 scipy.filters is now only optional to run ImageAnalyzer
 457 </p>
 458 </li>
 459 <li>
 460 <p>
 461 ImageAnalyzer: Allow to change aspect ratio for images in ImageAnalyzer (via
 462   the pixel dimesion dialog)
 463 </p>
 464 </li>
 465 <li>
 466 <p>
 467 ImageAnalyzer: Zemax file format loading fixes and autodetection improvements.
 468 </p>
 469 </li>
 470 </ul>
 471 <h3>0.1-alpha7</h3>
 472 <p>Only Plotfile2 changes in this release. Various speed-up and code optimization, and the support for changing also the color for all line-plot elements.</p>
 473 <h3>0.1-alpha6</h3>
 474 <p>This is the first version of PyPlotSuite released as a single tarball. It
 475 includes both ImageAnalyzer and Plotfile2.</p>
 476 <p>A new plot property dialog in Plotfile2 allows to change many plot parameters
 477 (line style and width, marker style and size). There's also the GUI for
 478 changing the colors of the various plot elements but this functions is not
 479 implemented in the underlying code yet.</p>
 480 </div>
 481 <h2>Release Notice</h2>
 482 <div class="sectionbody">
 483 <p>Early versions of <strong>ImageAnalyzer</strong> and <strong>Plotfile2</strong> were released in separated
 484 tarballs with separated version number. Now they are released together in the
 485 same tarball with the same version number (and I plan to integrate them more).
 486 However they retain separated changelogs, so you can keep track of each
 487 application separately.</p>
 488 </div>
 489 <h2>Installation</h2>
 490 <div class="sectionbody">
 491 <p>You can decompress the archive where you want and then execute PyPloSuite in
 492 place, entering the directory and typing:</p>
 493 <div class="listingblock">
 494 <div class="content">
 495 <pre><tt>  python imageanalyzer</tt></pre>
 496 </div></div>
 497 <p>or</p>
 498 <div class="listingblock">
 499 <div class="content">
 500 <pre><tt>  python plotfile2</tt></pre>
 501 </div></div>
 502 <p>You can install PyPlotSuite system wide with this command:</p>
 503 <div class="listingblock">
 504 <div class="content">
 505 <pre><tt>  python setup.py install</tt></pre>
 506 </div></div>
 507 </div>
 508 <h2>Development Version</h2>
 509 <div class="sectionbody">
 510 <p>The development version of <strong>PyPlotSuite</strong> is hosted on a
 511 <a href="http://repo.or.cz/w/pyplotsuite.git">git repository</a>. To download the latest
 512 development version just install <a href="http://git.or.cz/">git</a>
 513 and type:</p>
 514 <div class="listingblock">
 515 <div class="content">
 516 <pre><tt>  $ git clone git://repo.or.cz/pyplotsuite.git</tt></pre>
 517 </div></div>
 518 <p>Now you have a complete working tree of PyPlotSuite to test/hack on. If git
 519 and cogito does not work on your OS (I think only windows is affected) look at
 520 <a href="http://bazaar-vcs.org/">bazar</a> that is multiplatform SCM with a git plugin too.</p>
 521 </div>
 522 <h2>Requirements</h2>
 523 <div class="sectionbody">
 524 <p>You must have this software installed in order to be able to run the program:</p>
 525 <ul>
 526 <li>
 527 <p>
 528 Any recent version of Linux, Mac OSX or Windows
 529 </p>
 530 </li>
 531 <li>
 532 <p>
 533 Python 2.4 or newer (2.3 may still work, not tested):
 534     <a href="http://www.python.org">http://www.python.org</a>
 535 </p>
 536 </li>
 537 <li>
 538 <p>
 539 PyGTK 2.x:
 540     <a href="http://www.pygtk.org/">http://www.pygtk.org/</a>
 541 </p>
 542 </li>
 543 <li>
 544 <p>
 545 NumPy (1.0 or newer)
 546     <a href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
 547 </p>
 548 </li>
 549 <li>
 550 <p>
 551 MatPlotLib (0.87 or newer):
 552     <a href="http://matplotlib.sourceforge.net/">http://matplotlib.sourceforge.net/</a>
 553 </p>
 554 </li>
 555 <li>
 556 <p>
 557 SciPy (only the module scipy.ndimage.filters):
 558     <a href="http://www.scipy.org/">http://www.scipy.org/</a>
 559 </p>
 560 </li>
 561 <li>
 562 <p>
 563 Python Image Library (PIL):
 564     <a href="http://www.pythonware.com/products/pil/">http://www.pythonware.com/products/pil/</a>
 565 </p>
 566 </li>
 567 </ul>
 568 <div class="admonitionblock">
 569 <table><tr>
 570 <td class="icon">
 571 <img src="./images/icons/note.png" alt="Note" />
 572 </td>
 573 <td class="content">Typically Numpy is a prerequisite for Matplotlib, so you may have
 574 installed it in bundle with Matplotlib.</td>
 575 </tr></table>
 576 </div>
 577 <div class="admonitionblock">
 578 <table><tr>
 579 <td class="icon">
 580 <img src="./images/icons/note.png" alt="Note" />
 581 </td>
 582 <td class="content">The Scipy module and the PIL library are a requirement only if you want
 583 to run ImageAnalyzer. Plotfile2 does not requires them.</td>
 584 </tr></table>
 585 </div>
 586 </div>
 587 <h2>Image Analyzer</h2>
 588 <div class="sectionbody">
 589 <div class="hlist"><table>
 590 <tr>
 591 <td class="hlist1">
 592 Name
 593 </td>
 594 <td class="hlist2">
 595 Image Analyzer
 596 </td>
 597 </tr>
 598 <tr>
 599 <td class="hlist1">
 600 Description
 601 </td>
 602 <td class="hlist2">
 603 A tool to extract and make measures on scientific images.
 604 </td>
 605 </tr>
 606 </table></div>
 607 <h3>Description</h3>
 608 <p>ImageAnalyzer is a python[1] program written with the purpose to analyze
 609 scientific images to extract information such dimensions, and to reveal some
 610 subtle features. You can also create and save publication quality figures in a
 611 variety of hard-copy formats (using Matplotlib[5]).</p>
 612 <p>To execute the program type:</p>
 613 <div class="listingblock">
 614 <div class="content">
 615 <pre><tt>  python imageanalyzer</tt></pre>
 616 </div></div>
 617 <p>Remeber to check the software requirement above.</p>
 618 <h3>Image formats supported</h3>
 619 <p>All format supported by the PIL[6] library, with the following pixel formats:
 620 - L (Luminance, aka black&amp;white) 8 bit and 14 bit
 621 - RBG(A) with 8bit per channel</p>
 622 <h3>Features</h3>
 623 <p>The features currently implemented are:</p>
 624 <ul>
 625 <li>
 626 <p>
 627 Load, zoom and navigate on any RBG(A) or L (Luminance, aka black&amp;white)
 628       images.
 629 </p>
 630 </li>
 631 <li>
 632 <p>
 633 The possibility to choose one of the following 17 interpolation
 634       algorithms:
 635           Bessel, Bicubic, Bilinear, Blackman, Catrom, Gaussian, Hamming,
 636           Hanning, Hermite, Kaiser, Lanczos, Mitchell, Nearest, Quadric, Sinc,
 637           Spline16, Spline36.
 638       The default one is Nearest which is "no interpolation".
 639 </p>
 640 </li>
 641 <li>
 642 <p>
 643 Select one of the 14 color-maps (only for L images).
 644 </p>
 645 </li>
 646 <li>
 647 <p>
 648 Select a dynamic range either numerically and graphically through an
 649       histogram of the image (only for L images).
 650 </p>
 651 </li>
 652 <li>
 653 <p>
 654 Grid on/off, black/white (to match various color-maps).
 655 </p>
 656 </li>
 657 <li>
 658 <p>
 659 Calculate the distance between two points with the option to set the pixel
 660       dimension for the image (x and y separately).
 661 </p>
 662 </li>
 663 <li>
 664 <p>
 665 Plot the pixel-precise profile of an arbitrary number of sections of the
 666       image (only for L images).
 667 </p>
 668 </li>
 669 </ul>
 670 <h3>ImageAnalyzer TODO</h3>
 671 <p>To-do list in no particular order:</p>
 672 <ul>
 673 <li>
 674 <p>
 675 Allow to save modified images.
 676 </p>
 677 </li>
 678 <li>
 679 <p>
 680 Allow to save/load plot properties (colormap, interpolation, zoom).
 681       Handle this as explained in Plotfile2 TODO (below).
 682 </p>
 683 </li>
 684 <li>
 685 <p>
 686 Allow to choose font size for title and labels (separately).
 687 </p>
 688 </li>
 689 <li>
 690 <p>
 691 Fix axis apect ratio in histogram window.
 692 </p>
 693 </li>
 694 <li>
 695 <p>
 696 Better handling of failure on file load.
 697 </p>
 698 </li>
 699 <li>
 700 <p>
 701 Use Plotfile2 (instead of the current custom window) to show image
 702       sections.
 703 </p>
 704 </li>
 705 <li>
 706 <p>
 707 More image filtering options.
 708 </p>
 709 </li>
 710 <li>
 711 <p>
 712 Add pixel-value picker tool.
 713 </p>
 714 </li>
 715 <li>
 716 <p>
 717 Peak integration tool (2d integration on an elliptical area).
 718 </p>
 719 </li>
 720 <li>
 721 <p>
 722 Noise removal tools (dithering, noise shaping, 2D matched filter, you
 723       name it! :D)
 724 </p>
 725 </li>
 726 </ul>
 727 </div>
 728 <h2>Plotfile2</h2>
 729 <div class="sectionbody">
 730 <div class="hlist"><table>
 731 <tr>
 732 <td class="hlist1">
 733 Name
 734 </td>
 735 <td class="hlist2">
 736 Plotfile2
 737 </td>
 738 </tr>
 739 <tr>
 740 <td class="hlist1">
 741 Description
 742 </td>
 743 <td class="hlist2">
 744 A tool plot 1D data series.
 745 </td>
 746 </tr>
 747 </table></div>
 748 <h3>Description</h3>
 749 <p>Plotfile2 is is a python[1] program written with the purpose to quick plot data
 750 series stored in standard ascii text files. Multiple data series can be plotted,
 751 compared and the resulting plot can be saved in a variety of image file formats
 752 with a customizable size and resolution. This feature come particularly handy
 753 if you want to embed your plot in a document and you what size the final image
 754 will have.</p>
 755 <p>Plotfile2 is written using the GTK toolkit[2] and embeds Matplotlib[5] plot
 756 facility.</p>
 757 <p>To execute the program, enter the Plotfile2 dir and type:</p>
 758 <div class="listingblock">
 759 <div class="content">
 760 <pre><tt>  python plotfile2</tt></pre>
 761 </div></div>
 762 <p>See also the software requirements above.</p>
 763 <h3>Features</h3>
 764 <p>At the moment Plotfile2 can:</p>
 765 <ul>
 766 <li>
 767 <p>
 768 Load one or more data series from a two column (spaces or tab separated)
 769       ascii file. Blank lines (only spaces or tabs) are ignored.
 770 </p>
 771 </li>
 772 <li>
 773 <p>
 774 Detect if there is an header to automatically set axis labels. The header
 775       must be one line with two strings separated by spacing (or tabs). Blank
 776       lines before and after the header are ignored. More than two
 777       space-separated string results in an error.
 778 </p>
 779 </li>
 780 <li>
 781 <p>
 782 Controls to change the X and Y axis range, scale (linear or
 783       log) and  toggle grid.
 784 </p>
 785 </li>
 786 <li>
 787 <p>
 788 Controls to toggle if plot shows points (markers), lines or both.
 789 </p>
 790 </li>
 791 <li>
 792 <p>
 793 Complete customization of plot elements through a dedicated dialog
 794       (line style, marker type, colors, etc&#8230;).
 795 </p>
 796 </li>
 797 <li>
 798 <p>
 799 Set the plot title and axis labels
 800 </p>
 801 </li>
 802 <li>
 803 <p>
 804 Set the figure size (both in inches or in cm) and resolution (in dpi).
 805       This is useful to export a plot to be included in a document with a know
 806       size.
 807 </p>
 808 </li>
 809 <li>
 810 <p>
 811 Navigate/explore plots (zoom, un-zoom, pan, etc) thanks to the Matplotlib
 812       NavigationToolbar2 (try to click on the crossed arrows icon and then
 813       click and dragg with the right mouse button).
 814 </p>
 815 </li>
 816 <li>
 817 <p>
 818 Save the plot in a multitude of image formats (png, jpeg, eps, pdf, &#8230;
 819       all the formats supported by Matplotlib). Just click on the floppy icon.
 820 </p>
 821 </li>
 822 </ul>
 823 <h3>Plotfile2 TODO</h3>
 824 <ul>
 825 <li>
 826 <p>
 827 Possibility to customize plot line style, line color, line width, marker
 828   color, marker size, marker type for each series. <strong>[COMPLETED]</strong>
 829 </p>
 830 </li>
 831 <li>
 832 <p>
 833 Possibility to use spline interpolation (with various orders), and
 834   exponential-spline interpolation <em>[Work in progress]</em>.
 835 </p>
 836 </li>
 837 <li>
 838 <p>
 839 Add dialogs to choose an arbitrary color for plot elements in
 840   the "Plot Properties" dialog.
 841 </p>
 842 </li>
 843 <li>
 844 <p>
 845 Allow font size (and if possible) font style change for labels and title.
 846 </p>
 847 </li>
 848 <li>
 849 <p>
 850 Save plots as data (two columns ascii file or csv). This is useful for
 851   new data generated by the interpolation.
 852 </p>
 853 </li>
 854 <li>
 855 <p>
 856 Allow to save and load plot properties associated with a set of data. This
 857   would allow to load a dataset with associated plot style. To maintain the
 858   data in a compatible format this metadata will be saved in a new file with
 859   same name but different extension (f.e. ".plot"). Maybe the file should
 860   be hidden&#8230; (in the same dir of the data of course).
 861 </p>
 862 </li>
 863 <li>
 864 <p>
 865 Add basic operators (spectrum, intergrate, differentiate: which make sense?).
 866 </p>
 867 </li>
 868 <li>
 869 <p>
 870 Embed an (optional) [i]python shell.
 871 </p>
 872 </li>
 873 </ul>
 874 <h3>Plotfile2 Known Problems</h3>
 875 <ul>
 876 <li>
 877 <p>
 878 When you change figure size and resolution using the dedicated dialog, the
 879   main window may show a scrambled plot (or only an corner of the entire plot).
 880   This is only a visualization issue. Therefore, if you save the file (without
 881   resizing the window!) you will obtain the image file with the correct size
 882   and resolution ready to be included in your documents.
 883 </p>
 884 </li>
 885 </ul>
 886 <div class="admonitionblock">
 887 <table><tr>
 888 <td class="icon">
 889 <img src="./images/icons/note.png" alt="Note" />
 890 </td>
 891 <td class="content">If you have any suggestion to solve this problem please contact
 892 <a href="mailto:tritemio@gmail.com">me</a> via mail.</td>
 893 </tr></table>
 894 </div>
 895 </div>
 896 <h2>Links</h2>
 897 <div class="sectionbody">
 898 <ol>
 899 <li>
 900 <p>
 901 <strong>Python</strong>: a dynamic object-oriented programming language.
 902 </p>
 903 <ul>
 904 <li>
 905 <p>
 906 <a href="http://www.python.org">http://www.python.org</a>
 907 </p>
 908 </li>
 909 </ul>
 910 </li>
 911 <li>
 912 <p>
 913 <strong>PyGTK</strong>: Python binding for the GTK user interface library.
 914 </p>
 915 <ul>
 916 <li>
 917 <p>
 918 <a href="http://www.pygtk.org/">http://www.pygtk.org/</a>
 919 </p>
 920 </li>
 921 </ul>
 922 </li>
 923 <li>
 924 <p>
 925 <strong>Numpy</strong>: The fundamental package needed for numerical computing with Python.
 926     It is the successor (and unifier) of all the old projects (Numeric and
 927     Numarray) for python numerical computing.
 928 </p>
 929 <ul>
 930 <li>
 931 <p>
 932 <a href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
 933 </p>
 934 </li>
 935 </ul>
 936 </li>
 937 <li>
 938 <p>
 939 <strong>SciPy</strong>: Many modules that were not specific to Numpy are gathered under the
 940     broader project SciPy:
 941 </p>
 942 <ul>
 943 <li>
 944 <p>
 945 <a href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
 946 </p>
 947 </li>
 948 </ul>
 949 </li>
 950 <li>
 951 <p>
 952 <strong>MatPlotLib</strong>: A python 2D plotting library which produces publication quality
 953     figures in a variety of hard-copy formats and interactive environments
 954     across platforms.
 955 </p>
 956 <ul>
 957 <li>
 958 <p>
 959 <a href="http://matplotlib.sourceforge.net/">http://matplotlib.sourceforge.net/</a>
 960 </p>
 961 </li>
 962 </ul>
 963 </li>
 964 <li>
 965 <p>
 966 <strong>Python Imaging Library</strong> (PIL).
 967 </p>
 968 <ul>
 969 <li>
 970 <p>
 971 <a href="http://www.pythonware.com/products/pil/">http://www.pythonware.com/products/pil/</a>
 972 </p>
 973 </li>
 974 </ul>
 975 </li>
 976 </ol>
 977 <div class="sidebarblock">
 978 <div class="sidebar-content">
 979 <p>The html version of this README was generated from the ASCII file with:</p>
 980 <div class="listingblock">
 981 <div class="content">
 982 <pre><tt>$ asciidoc -a toc -a icons -a badges README.txt</tt></pre>
 983 </div></div>
 984 </div></div>
 985 </div>
 986 <div id="footer">
 987 <div id="footer-text">
 988 Last updated 28-Jul-2007 16:43:22 CEST
 989 </div>
 990 <div id="footer-badges">
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