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Overview
Comment: | Updated the "Image Format vs Fossil Repo Size" doc and its associated notebook and SVG file: smarter initial repo size handling so we don't have to throw away the first 3 rows of data; now works with Anaconda, allowing simpler local replication of results; using /tmp for the test instead of relying on "open --nested" to protect us from running the experiment in-tree; clarified discussion of results. |
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User & Date: | wyoung 2020-06-26 21:49:56.919 |
Context
2020-06-26
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23:06 | Attempt to improve the look of the forum when using the 'eagle' skin. ... (check-in: 9cb1556e user: mistachkin tags: trunk) | |
21:49 | Updated the "Image Format vs Fossil Repo Size" doc and its associated notebook and SVG file: smarter initial repo size handling so we don't have to throw away the first 3 rows of data; now works with Anaconda, allowing simpler local replication of results; using /tmp for the test instead of relying on "open --nested" to protect us from running the experiment in-tree; clarified discussion of results. ... (check-in: f281b3df user: wyoung tags: trunk) | |
2020-06-25
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13:32 | Add a link to the built-in help to the permuted documentation index. ... (check-in: db90281c user: drh tags: trunk) | |
Changes
Changes to www/image-format-vs-repo-size.ipynb.
1 2 3 4 5 6 7 8 9 10 | { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Image Format vs Fossil Repository Size\n", "\n", "## Prerequisites\n", "\n", | | > > | < > > > | | | | | | > > > > > | > > > > > > > > > | > > | | > > > > > > > > > > < < | | | | > > < | | < < | | | | > > | | | | | < < > > > | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | < | | > | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | > > > | > > > > > > > | > > > > > > > | > > > > > > > | | > > > | > > > > > | | | | > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 | { "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Image Format vs Fossil Repository Size\n", "\n", "## Prerequisites\n", "\n", "This notebook was originally developed with standalone [JupyterLab] and Python 2 but was later moved to JupyterLab under [Anaconda] with Python 3. Backporting to Python 2 may require manual adjustment. Getting it running under stock JupyterLab or plain-old-Jupyter should be straightforward for one familiar with the tools. We will assume you're following in my footsteps, using Anaconda.\n", "\n", "One of the reasons we switched to Anaconda is that it comes with all but one of this notebook's prerequisites, that last remaining one of which you install so:\n", "\n", " $ pip install wand\n", "\n", "That should be done in a shell where \"`pip`\" is the version that came with Anaconda. Otherwise, the package will likely end up in some *other* Python package tree, which Anaconda's Python kernel may not be smart enough to find on its own.\n", "\n", "Note that you do *not* use `conda` for this: as of this writing, [Wand] is not available in a form that installs via `conda`.\n", "\n", "This notebook was written and tested on a macOS system where `/tmp` exists. Other platforms may require adjustments to the scripts below.\n", "\n", "[Anaconda]: https://www.anaconda.com/distribution/\n", "[JupyterLab]: https://github.com/jupyterlab/\n", "[Wand]: http://wand-py.org/\n", "\n", "\n", "## Running\n", "\n", "The next cell generates the test repositories. This takes about 3 seconds to run on my machine. If you have to uncomment the \"`sleep`\" call in the inner loop, this will go up to about 45 seconds.\n", "\n", "The next cell produces the bar chart from the collected data, all but instantaneously.\n", "\n", "This split allows you to generate the expensive experimental data in a single pass, then play as many games as you like with the generated data.\n", "\n", "\n", "## Discussion\n", "\n", "That is kept in [a separate document](image-format-vs-repo-size.md) so we can share that document with Fossil's Markdown renderer." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Created test directory /tmp/image-format-vs-repo-size\n", "Created ../test-jpeg.fossil for format JPEG.\n", "Created ../test-bmp.fossil for format BMP.\n", "Created ../test-tiff.fossil for format TIFF.\n", "Created ../test-png.fossil for format PNG.\n", "Experiment completed in 3.0627901554107666 seconds.\n" ] } ], "source": [ "import os\n", "import random\n", "import subprocess\n", "import time\n", "\n", "from wand.color import Color\n", "from wand.drawing import Drawing\n", "from wand.image import Image\n", "\n", "import pandas as pd\n", "\n", "size = 256\n", "iterations = 10\n", "start = time.time()\n", "repo_sizes = []\n", "fossil = '/usr/local/bin/fossil'\n", "\n", "if not os.path.isfile(fossil): raise RuntimeError(\"No such executable \" + fossil)\n", "if not os.access(fossil, os.X_OK): raise RuntimeError(\"Cannot execute \" + fossil)\n", "\n", "tdir = os.path.join('/tmp', 'image-format-vs-repo-size')\n", "if not os.path.isdir(tdir): os.mkdir(tdir, 0o700)\n", "print(\"Created test directory \" + tdir)\n", " \n", "formats = ['JPEG', 'BMP', 'TIFF', 'PNG']\n", "for f in formats:\n", " ext = f.lower()\n", " wdir = os.path.join(tdir, 'work-' + ext)\n", " if not os.path.isdir(wdir): os.mkdir(wdir, 0o700)\n", " os.chdir(wdir)\n", " repo = '../test-' + ext + '.fossil'\n", " ifn = 'test.' + ext\n", " ipath = os.path.join(wdir, ifn)\n", " rs = []\n", " \n", " def add_repo_size():\n", " rs.append(os.path.getsize(repo) / 1024.0 / 1024.0)\n", " \n", " def set_repo_page_size(n):\n", " subprocess.run([\n", " fossil,\n", " 'rebuild',\n", " '--compress',\n", " '--pagesize',\n", " str(n),\n", " '--vacuum'\n", " ])\n", "\n", " try:\n", " # Create test repo\n", " subprocess.run([fossil, 'init', repo])\n", " subprocess.run([fossil, 'open', repo])\n", " subprocess.run([fossil, 'set', 'binary-glob', \"*.{0}\".format(ext)])\n", " set_repo_page_size(512) # minimum\n", " add_repo_size()\n", " set_repo_page_size(8192) # default\n", " print(\"Created \" + repo + \" for format \" + f + \".\")\n", "\n", " # Create test image and add it to the repo\n", " img = Image(width = size, height = size, depth = 8,\n", " background = 'white')\n", " img.alpha_channel = 'remove'\n", " img.evaluate('gaussiannoise', 1.0)\n", " img.save(filename = ipath)\n", " subprocess.run([fossil, 'add', ifn])\n", " subprocess.run([fossil, 'ci', '-m', 'initial'])\n", " #print(\"Added initial \" + f + \" image.\")\n", " add_repo_size()\n", "\n", " # Change a random pixel to a random RGB value and check it in\n", " # $iterations times.\n", " for i in range(iterations - 1):\n", " with Drawing() as draw:\n", " x = random.randint(0, size - 1)\n", " y = random.randint(0, size - 1)\n", "\n", " r = random.randint(0, 255)\n", " g = random.randint(0, 255)\n", " b = random.randint(0, 255)\n", " \n", " draw.fill_color = Color('rgb({0},{1},{2})'.format(\n", " r, g, b\n", " ))\n", " draw.color(x, y, 'point')\n", " draw(img)\n", " img.save(filename = ipath)\n", " \n", " # You might need to uncomment the next line if you find that\n", " # the repo size doesn't change as expected. In some versions\n", " # of Wand (or is it the ImageMagick underneath?) we have seen\n", " # what appear to be asynchronous saves, with a zero-length file\n", " # here if you don't wait for the save to complete.\n", " #time.sleep(1.0)\n", " \n", " subprocess.run([fossil, 'ci', '-m', '\"change {0} step {1}'.format(\n", " f, i\n", " )])\n", " add_repo_size()\n", " \n", " # Repo complete for this format\n", " repo_sizes.append(pd.Series(rs, name=f))\n", "\n", " finally:\n", " if os.path.exists(ipath): os.remove(ipath)\n", " if os.path.exists(tdir):\n", " if os.path.isfile(repo):\n", " subprocess.run([fossil, 'close', '-f'])\n", " os.unlink(repo)\n", " os.chdir(tdir);\n", " os.rmdir(wdir)\n", " if os.path.exists(repo): os.remove(repo)\n", " \n", "print(\"Experiment completed in \" + str(time.time() - start) + \" seconds.\")" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "image/svg+xml": [ "<?xml version=\"1.0\" encoding=\"utf-8\" 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Changes to www/image-format-vs-repo-size.md.
1 2 3 4 5 | # Image Format vs Fossil Repo Size ## The Problem Fossil has a [delta compression][dc] feature which removes redundant | | < | | < | | | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | # Image Format vs Fossil Repo Size ## The Problem Fossil has a [delta compression][dc] feature which removes redundant information from a file relative to its parent on check-in.¹ That delta is then [zlib][zl]-compressed before being stored in the Fossil repository database file. Storing pre-compressed data files in a Fossil repository defeats both of these space-saving measures: 1. Binary data compression algorithms turn the file data into [pseudorandom noise][prn].² Typical data compression algorithms are not [hash functions][hf], where the goal is that a change to each bit in the input has a statistically even chance of changing every bit in the output, but because they do approach that pathological condition, pre-compressed data tends to defeat Fossil’s delta compression algorithm, there being so little correlation between two different outputs from the binary data compression algorithm. 2. An ideal lossless binary data compression algorithm cannot be applied more than once to make the data even smaller, since random noise is incompressible. The consequence for our purposes here is that pre-compressed data doesn’t benefit from Fossil’s zlib compression. You might then ask, what does it matter if the space savings comes from the application file format (e.g. JPEG, DOCX, Zip, etc.) or from Fossil itself? It really doesn’t, as far as point 2 above goes, but point 1 causes the Fossil repository to balloon out of proportion to the size of the input data change on each checkin. This article will illustrate that problem, quantify it, and give a solution to it. [dc]: ./delta_format.wiki [hf]: https://en.wikipedia.org/wiki/Hash_function |
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48 49 50 51 52 53 54 | this article’s advice also applies to many other file types. For just a few examples out of what must be thousands: * **Microsoft Office**: The [OOXML document format][oox] used from Office 2003 onward (`.docx`, `.xlsx`, `.pptx`, etc.) are Zip files containing an XML document file and several collateral files. | | | | 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 | this article’s advice also applies to many other file types. For just a few examples out of what must be thousands: * **Microsoft Office**: The [OOXML document format][oox] used from Office 2003 onward (`.docx`, `.xlsx`, `.pptx`, etc.) are Zip files containing an XML document file and several collateral files. * **Libre Office**: For the purposes of this article, its [OpenDocument Format][odf] is designed the same basic way as OOXML. * **Java**: A Java [`.jar` file][jcl] is a Zip file containing JVM `.class` files, manifest files, and more. * **Windows Installer:** An [`*.msi` file][wi] is a proprietary database format that contains, among other things, [Microsoft Cabinet][cab]-compressed files, which in turn may hold Windows |
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76 77 78 79 80 81 82 | [wi]: https://en.wikipedia.org/wiki/Windows_Installer ## Demonstration The companion `image-format-vs-repo-size.ipynb` file ([download][nbd], | | | | | | | > > | > > > > > > > > > | 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 | [wi]: https://en.wikipedia.org/wiki/Windows_Installer ## Demonstration The companion `image-format-vs-repo-size.ipynb` file ([download][nbd], [preview][nbp]) is a [JupyterLab][jl] notebook implementing the following experiment: 1. Create a new minimum-size Fossil repository. Save this initial size. 2. Use [ImageMagick][im] via [Wand][wp] to generate a JPEG file of a particular size — currently 256 px² — filled with Gaussian noise to make data compression more difficult than with a solid-color image. 3. Check that image into the new Fossil repo, and remember that size. 4. Change a random pixel in the image to a random RGB value, save that image, check it in, and remember the new Fossil repo size. 5. Iterate on step 4 some number of times — currently 10 — and remember the Fossil repo size at each step. 6. Repeat the above steps for BMP, TIFF,³ and PNG. 7. Create a bar chart showing how the Fossil repository size changes with each checkin. We chose to use JupyterLab for this because it makes it easy for you to modify the notebook to try different things. Want to see how the results change with a different image size? Easy, change the `size` value in the second cell of the notebook. Want to try more image formats? You can put anything ImageMagick can recognize into the `formats` list. Want to find the break-even point for images like those in your own repository? Easily done with a small amount of code. [im]: https://www.imagemagick.org/ [jl]: https://jupyter.org/ [nbd]: ./image-format-vs-repo-size.ipynb [nbp]: https://nbviewer.jupyter.org/urls/fossil-scm.org/fossil/doc/trunk/www/image-format-vs-repo-size.ipynb [wp]: http://wand-py.org/ ## Results Running the notebook gives a bar chart something like⁴ this:  There are a few key things we want to draw your attention to in that chart: * BMP and uncompressed TIFF are nearly identical in size for all checkins, and the repository growth rate is negligible past the first commit.⁵ We owe this economy to Fossil’s delta compression feature: it is encoding each of those single-pixel changes in a very small amount of repository space. * The JPEG and TIFF bars increase by large amounts on most checkins even though each checkin *also* encodes only a *single-pixel change*. * The size of the first checkin in the BMP and TIFF cases is roughly the same as that for the PNG case, because both PNG and Fossil use the zlib binary data compression algorithm. This shows that for repos where the image files are committed only once, there is virtually no penalty to using BMP or TIFF over PNG. The file sizes likely differ only because of differences in zlib settings between the cases. * Because JPEG’s lossy nature allows it to start smaller and have smaller size increases than than PNG, the crossover point with BMP/TIFF isn’t until 7-9 checkins in typical runs of this [Monte Carlo experiment][mce]. Given a choice among these four file formats and a willingness to use lossy image compression, a rational tradeoff is to choose JPEG for repositories where each image will change fewer than that number of times. [mce]: https://en.wikipedia.org/wiki/Monte_Carlo_method ## Automated Recompression Since programs that produce and consume binary-compressed data files |
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233 234 235 236 237 238 239 | here. ---- ## Footnotes and Digressions | > | | > > | | | | | > | | | | < < < | > > | < < > > > | | < < > | 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 | here. ---- ## Footnotes and Digressions 1. This problem is not Fossil-specific. Several other programs also do delta compression, so they’ll also be affected by this problem: [rsync][rs], [Unison][us], [Git][git], etc. You should take this article’s advice when using all such programs, not just Fossil. When using file copying and synchronization programs *without* delta compression, on the other hand, it’s best to use the most highly-compressed file format you can tolerate, since they copy the whole file any time any bit of it changes. 2. In fact, a good way to gauge the effectiveness of a given compression scheme is to run its output through the same sort of tests we use to gauge how “random” a given [PRNG][prng] is. Another way to look at it is that if there is a discernible pattern in the output of a compression scheme, that constitutes *information* (in [the technical sense of that word][ith]) that could be further compressed. 3. We're using *uncompressed* TIFF here, not [LZW][lzw]- or Zip-compressed TIFF, either of which would give similar results to PNG, which is always zlib-compressed. 4. The raw data changes somewhat from one run to the next due to the use of random noise in the image to make the zlib/PNG compression more difficult, and the random pixel changes. Those test design choices make this a [Monte Carlo experiment][mce]. We’ve found that the overall character of the results doesn’t change from one run to the next. 5. It’s not clear to me why there is a one-time jump in size for BMP and TIFF past the first commit. I suspect it is due to the SQLite indices being initialized for the first time. Page size inflation might have something to do with it as well, though we tried to control that by rebuilding the initial DB with a minimal page size. If you re-run the program often enough, you will sometimes see the BMP or TIFF bar jump higher than the other, again likely due to one of the repos crossing a page boundary. Another curious artifact in the data is that the BMP is slightly larger than for the TIFF. This goes against expectation because a low-tech format like BMP should have a small edge in this test because TIFF metadata includes the option for multiple timestamps, UUIDs, etc., which bloat the checkin size by creating many small deltas. 6. The `Makefile` above is not battle-tested. Please report bugs and needed extensions [on the forum][for]. [for]: https://fossil-scm.org/forum/forumpost/15e677f2c8 [git]: https://git-scm.com/ [ith]: https://en.wikipedia.org/wiki/Information_theory [lzw]: https://en.wikipedia.org/wiki/Lempel%E2%80%93Ziv%E2%80%93Welch [prng]: https://en.wikipedia.org/wiki/Pseudorandom_number_generator [rs]: https://rsync.samba.org/ [us]: http://www.cis.upenn.edu/~bcpierce/unison/ |
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