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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 produced 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-alpha7
 433 </td>
 434 </tr>
 435 </table></div>
 436 </div>
 437 <h2>NEWS</h2>
 438 <div class="sectionbody">
 439 <h3>0.1-alpha7</h3>
 440 <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>
 441 <h3>0.1-alpha6</h3>
 442 <p>This is the first version of PyPlotSuite released as a single tarball. It
 443 includes both ImageAnalyzer and Plotfile2.</p>
 444 <p>A new plot property dialog in Plotfile2 allows to change many plot parameters
 445 (line style and width, marker style and size). There's also the GUI for
 446 changing the colors of the various plot elements but this functions is not
 447 implemented in the underlying code yet.</p>
 448 </div>
 449 <h2>Release Notice</h2>
 450 <div class="sectionbody">
 451 <p>Early versions of <strong>ImageAnalyzer</strong> and <strong>Plotfile2</strong> were released in separated
 452 tarballs with separated version number. Now they are released together in the
 453 same tarball with the same version number (and I plan to integrate them more).
 454 However they retain separated changelogs, so you can keep track of each
 455 application separately.</p>
 456 <p>The development version of <strong>PyPlotSuite</strong> is hosted on a
 457 <a href="http://repo.or.cz/w/pyplotsuite.git">git repository</a>. To download the latest
 458 (possibly broken) development version just install <a href="http://git.or.cz/">git</a>
 459 and type:</p>
 460 <div class="listingblock">
 461 <div class="content">
 462 <pre><tt>$ git clone ssh://repo.or.cz/srv/git/pyplotsuite.git</tt></pre>
 463 </div></div>
 464 <p>Now you have a complete working version of PyPlotSuite to test/hack on. If git
 465 and cogito does not work on your OS (i.e. windows) look at
 466 <a href="http://bazaar-vcs.org/">bazar</a> that is multiplatform SCM with a git plugin too.</p>
 467 </div>
 468 <h2>Requirements</h2>
 469 <div class="sectionbody">
 470 <p>You must have this software installed in order to be able to run the program:</p>
 471 <ul>
 472 <li>
 473 <p>
 474 Any recent version of Linux, Mac OSX or Windows
 475 </p>
 476 </li>
 477 <li>
 478 <p>
 479 Python 2.4 or newer (2.3 may still work, not tested):
 480     <a href="http://www.python.org">http://www.python.org</a>
 481 </p>
 482 </li>
 483 <li>
 484 <p>
 485 PyGTK 2.x:
 486     <a href="http://www.pygtk.org/">http://www.pygtk.org/</a>
 487 </p>
 488 </li>
 489 <li>
 490 <p>
 491 NumPy (1.0 or newer)
 492     <a href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
 493 </p>
 494 </li>
 495 <li>
 496 <p>
 497 MatPlotLib (0.87 or newer):
 498     <a href="http://matplotlib.sourceforge.net/">http://matplotlib.sourceforge.net/</a>
 499 </p>
 500 </li>
 501 <li>
 502 <p>
 503 SciPy (only the module scipy.ndimage.filters):
 504     <a href="http://www.scipy.org/">http://www.scipy.org/</a>
 505 </p>
 506 </li>
 507 <li>
 508 <p>
 509 Python Image Library (PIL):
 510     <a href="http://www.pythonware.com/products/pil/">http://www.pythonware.com/products/pil/</a>
 511 </p>
 512 </li>
 513 </ul>
 514 <div class="admonitionblock">
 515 <table><tr>
 516 <td class="icon">
 517 <img src="./images/icons/note.png" alt="Note" />
 518 </td>
 519 <td class="content">Typically Numpy is a prerequisite for Matplotlib, so you may have
 520 installed it in bundle with Matplotlib.</td>
 521 </tr></table>
 522 </div>
 523 <div class="admonitionblock">
 524 <table><tr>
 525 <td class="icon">
 526 <img src="./images/icons/note.png" alt="Note" />
 527 </td>
 528 <td class="content">The Scipy module and the PIL library are a requirement only if you want
 529 to run ImageAnalyzer. Plotfile2 does not requires them.</td>
 530 </tr></table>
 531 </div>
 532 </div>
 533 <h2>Image Analyzer</h2>
 534 <div class="sectionbody">
 535 <div class="hlist"><table>
 536 <tr>
 537 <td class="hlist1">
 538 Name
 539 </td>
 540 <td class="hlist2">
 541 Image Analyzer
 542 </td>
 543 </tr>
 544 <tr>
 545 <td class="hlist1">
 546 Description
 547 </td>
 548 <td class="hlist2">
 549 A tool to extract and make measures on scientific images.
 550 </td>
 551 </tr>
 552 </table></div>
 553 <h3>Description</h3>
 554 <p>ImageAnalyzer is a python[1] program written with the purpose to analyze
 555 scientific images to extract information such dimensions, and to reveal some
 556 subtle features. You can also create and save publication quality figures in a
 557 variety of hard-copy formats (using Matplotlib[5]).</p>
 558 <p>To execute the program type:</p>
 559 <div class="listingblock">
 560 <div class="content">
 561 <pre><tt>  python imageanalyzer.py</tt></pre>
 562 </div></div>
 563 <p>Remeber to check the software requirement above.</p>
 564 <h3>Image formats supported</h3>
 565 <p>All format supported by the PIL[6] library, with the following pixel formats:
 566 - L (Luminance, aka black&amp;white) 8 bit and 14 bit
 567 - RBG(A) with 8bit per channel</p>
 568 <h3>Features</h3>
 569 <p>The features currently implemented are:</p>
 570 <ul>
 571 <li>
 572 <p>
 573 Load, zoom and navigate on any RBG(A) or L (Luminance, aka black&amp;white)
 574       images.
 575 </p>
 576 </li>
 577 <li>
 578 <p>
 579 The possibility to choose one of the following 17 interpolation algorithms:
 580           Bessel, Bicubic, Bilinear, Blackman, Catrom, Gaussian, Hamming,
 581           Hanning, Hermite, Kaiser, Lanczos, Mitchell, Nearest, Quadric, Sinc,
 582           Spline16, Spline36.
 583       The default one is Nearest which is, in a way, "absence of interpolation".
 584 </p>
 585 </li>
 586 <li>
 587 <p>
 588 Select one of the 14 color-maps (only for L images)
 589 </p>
 590 </li>
 591 <li>
 592 <p>
 593 Select a dynamic range either numerically and graphically through an
 594       histogram of the image (only for L images).
 595 </p>
 596 </li>
 597 <li>
 598 <p>
 599 Grid on/off, black/white (to match various color-maps).
 600 </p>
 601 </li>
 602 <li>
 603 <p>
 604 Calculate the distance between two points with the option to set the pixel
 605       dimension for the image (x and y separately).
 606 </p>
 607 </li>
 608 <li>
 609 <p>
 610 Plot the pixel-precise profile of an arbitrary number of sections of the
 611       image (only for L images).
 612 </p>
 613 </li>
 614 </ul>
 615 </div>
 616 <h2>Plotfile2</h2>
 617 <div class="sectionbody">
 618 <div class="hlist"><table>
 619 <tr>
 620 <td class="hlist1">
 621 Name
 622 </td>
 623 <td class="hlist2">
 624 Plotfile2
 625 </td>
 626 </tr>
 627 <tr>
 628 <td class="hlist1">
 629 Description
 630 </td>
 631 <td class="hlist2">
 632 A tool plot 1D data series.
 633 </td>
 634 </tr>
 635 </table></div>
 636 <h3>Description</h3>
 637 <p>Plotfile2 is is a python[1] program written with the purpose to quick plot data
 638 series stored in standard ascii text files. Multiple data series can be plotted,
 639 compared and the resulting plot can be saved in a variety of image file formats
 640 with a customizable size and resolution. This feature come particularly handy
 641 if you want to embed your plot in a document and you what size the final image
 642 will have.</p>
 643 <p>Plotfile2 is written using the GTK toolkit[2] and embeds Matplotlib[5] plot
 644 facility.</p>
 645 <p>To execute the program, enter the Plotfile2 dir and type:</p>
 646 <div class="listingblock">
 647 <div class="content">
 648 <pre><tt>  python plotfile2.py</tt></pre>
 649 </div></div>
 650 <p>See also the software requirements above.</p>
 651 <h3>Features</h3>
 652 <p>At the moment Plotfile2 can:</p>
 653 <ul>
 654 <li>
 655 <p>
 656 Load one or more data series from a two column (spaces or tab separated)
 657       ascii file. Blank lines (only spaces or tabs) are ignored.
 658 </p>
 659 </li>
 660 <li>
 661 <p>
 662 Detect if there is an header to automatically set axis labels. The header
 663       must be a line with two strings separated by spacing (or tabs). Blank
 664       lines before and after the header are ignored. More than two
 665       space-separated string results in an error.
 666 </p>
 667 </li>
 668 <li>
 669 <p>
 670 Controls to change the X and Y axis range, scale (linear or log) and
 671       toggle grid.
 672 </p>
 673 </li>
 674 <li>
 675 <p>
 676 Controls to toggle if plot shows points (markers), lines or both.
 677 </p>
 678 </li>
 679 <li>
 680 <p>
 681 Complete customization of plot elements through a dedicated dialog
 682       (line style, marker type, colors).
 683 </p>
 684 </li>
 685 <li>
 686 <p>
 687 Set the plot title and axis labels
 688 </p>
 689 </li>
 690 <li>
 691 <p>
 692 Set the figure size (both in inches or in cm) and resolution (in dpi).
 693       This is useful to export a plot to be included in a document with a know
 694       size.
 695 </p>
 696 </li>
 697 <li>
 698 <p>
 699 Navigate/explore plots (zoom, un-zoom, pan, etc) with the Matplotlib
 700       NavigationToolbar2.
 701 </p>
 702 </li>
 703 <li>
 704 <p>
 705 Save the plot in a multitude of image formats (png, jpeg, eps, pdf, &#8230;
 706       all the formats supported by Matplotlib)
 707 </p>
 708 </li>
 709 </ul>
 710 <h3>Plotfile2 Roadmap</h3>
 711 <ul>
 712 <li>
 713 <p>
 714 Possibility to customize plot line style, line color, line width, marker
 715   color, marker size, marker type for each series. <strong>[COMPLETED]</strong>
 716 </p>
 717 </li>
 718 <li>
 719 <p>
 720 Possibility to use spline interpolation (with various orders), and
 721   exponential-spline interpolation.
 722 </p>
 723 </li>
 724 </ul>
 725 <h3>Plotfile2 Known Problems</h3>
 726 <ul>
 727 <li>
 728 <p>
 729 When you change figure size and resolution using the dedicated dialog, the
 730   main window may show a scrambled plot (or only an corner of the entire plot).
 731   This is only a visualization issue. Therefore, if you save the file (without
 732   resizing the window!) you will obtain the image file with the correct size
 733   and resolution ready to be included in your documents.
 734 </p>
 735 </li>
 736 </ul>
 737 <div class="admonitionblock">
 738 <table><tr>
 739 <td class="icon">
 740 <img src="./images/icons/note.png" alt="Note" />
 741 </td>
 742 <td class="content">If you have any suggestion to solve this problem please contact mailto:
 743 tritemio@gmail.com[me] via mail.</td>
 744 </tr></table>
 745 </div>
 746 </div>
 747 <h2>Links</h2>
 748 <div class="sectionbody">
 749 <ol>
 750 <li>
 751 <p>
 752 <strong>Python</strong>: a dynamic object-oriented programming language.
 753 </p>
 754 <ul>
 755 <li>
 756 <p>
 757 <a href="http://www.python.org">http://www.python.org</a>
 758 </p>
 759 </li>
 760 </ul>
 761 </li>
 762 <li>
 763 <p>
 764 <strong>PyGTK</strong>: Python binding for the GTK user interface library.
 765 </p>
 766 <ul>
 767 <li>
 768 <p>
 769 <a href="http://www.pygtk.org/">http://www.pygtk.org/</a>
 770 </p>
 771 </li>
 772 </ul>
 773 </li>
 774 <li>
 775 <p>
 776 <strong>Numpy</strong>: The fundamental package needed for numerical computing with Python.
 777     It is the successor (and unifier) of all the old projects (Numeric and
 778     Numarray) for python numerical computing.
 779 </p>
 780 <ul>
 781 <li>
 782 <p>
 783 <a href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
 784 </p>
 785 </li>
 786 </ul>
 787 </li>
 788 <li>
 789 <p>
 790 <strong>SciPy</strong>: Many modules that were not specific to Numpy are gathered under the
 791     broader project SciPy:
 792 </p>
 793 <ul>
 794 <li>
 795 <p>
 796 <a href="http://numpy.scipy.org/">http://numpy.scipy.org/</a>
 797 </p>
 798 </li>
 799 </ul>
 800 </li>
 801 <li>
 802 <p>
 803 <strong>MatPlotLib</strong>: A python 2D plotting library which produces publication quality
 804     figures in a variety of hard-copy formats and interactive environments
 805     across platforms.
 806 </p>
 807 <ul>
 808 <li>
 809 <p>
 810 <a href="http://matplotlib.sourceforge.net/">http://matplotlib.sourceforge.net/</a>
 811 </p>
 812 </li>
 813 </ul>
 814 </li>
 815 <li>
 816 <p>
 817 <strong>Python Imaging Library</strong> (PIL).
 818 </p>
 819 <ul>
 820 <li>
 821 <p>
 822 <a href="http://www.pythonware.com/products/pil/">http://www.pythonware.com/products/pil/</a>
 823 </p>
 824 </li>
 825 </ul>
 826 </li>
 827 </ol>
 828 <div class="sidebarblock">
 829 <div class="sidebar-content">
 830 <p>The html version of this README was generated from the ASCII file with:</p>
 831 <div class="listingblock">
 832 <div class="content">
 833 <pre><tt>$ asciidoc -a toc -a icons -a badges README</tt></pre>
 834 </div></div>
 835 </div></div>
 836 </div>
 837 <div id="footer">
 838 <div id="footer-text">
 839 Last updated 14-Jun-2007 18:53:15 CEST
 840 </div>
 841 <div id="footer-badges">
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