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Comment:Added "Image Format vs Fossil Repo Size" article and supporting files.
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SHA3-256:05f95db774b89fdc5c65fdee8591c5eddf23c74486ad1d16cc98eb9c81fed2c6
User & Date: wyoung 2019-03-24 17:25:28
Context
2019-03-24
18:50
Added my two recently-created documents to the permuted doc index check-in: 41579b4c user: wyoung tags: trunk
17:25
Added "Image Format vs Fossil Repo Size" article and supporting files. check-in: 05f95db7 user: wyoung tags: trunk
2019-03-23
21:47
Fix password change reported on Fossil Forum bug by ending the form tag properly. check-in: 643123d5 user: andybradford tags: trunk
Changes
Hide Diffs Unified Diffs Ignore Whitespace Patch

Added www/image-format-vs-repo-size.ipynb.















































































































































































































































































































































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{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Image Format vs Fossil Repository Size\n",
    "\n",
    "## Prerequisites\n",
    "\n",
    "`pip install jupyter matplotlib pandas wand`\n",
    "\n",
    "\n",
    "## Running\n",
    "\n",
    "The next cell generates the test repositories. This takes about half a minute due to the time needed for all the file I/O.\n",
    "\n",
    "The one after that produces the bar chart from the collected 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": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import random\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",
    "\n",
    "repo_sizes = []\n",
    "\n",
    "formats = ['JPEG', 'BMP', 'TIFF', 'PNG']\n",
    "for f in formats:\n",
    "    ext = f.lower()\n",
    "    tdir = 'test' + '-' + ext\n",
    "    repo = tdir + '.fossil'\n",
    "    ifn = 'test.' + ext\n",
    "    ipath = os.path.join(tdir, ifn)\n",
    "    rs = []\n",
    "    \n",
    "    def add_repo_size():\n",
    "        rs.append(os.path.getsize(repo) / 1024.0 / 1024.0)\n",
    "\n",
    "    try:\n",
    "        # Create test repo\n",
    "        if not os.path.exists(tdir): os.mkdir(tdir, 0700)\n",
    "        cmd = 'cd {0} ; fossil init ../{1} && fossil open ../{1} && fossil set binary-glob \"*.{2}\"'.format(\n",
    "            tdir, repo, ext\n",
    "        )\n",
    "        if os.system(cmd) != 0:\n",
    "            raise RuntimeError('Failed to create test repo ' + repo)\n",
    "        add_repo_size()\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",
    "        cmd = 'cd {0} ; fossil add {1} && fossil ci -m \"initial\"'.format(\n",
    "            tdir, ifn\n",
    "        )\n",
    "        if os.system(cmd) != 0:\n",
    "            raise RuntimeError('Failed to add ' + ifn + ' to test repo')\n",
    "        #print \"Created test repo \" + repo + \" for format \" + f + \".\"\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):\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",
    "                # ImageMagick appears to use some kind of asynchronous\n",
    "                # file saving mechanism, so we have to give it time to\n",
    "                # complete.\n",
    "                time.sleep(1.0)\n",
    "  \n",
    "                cmd = 'cd {0} ; fossil ci -m \"change {1} step {2}\"'.format(\n",
    "                    tdir, f, i\n",
    "                )\n",
    "                if os.system(cmd) != 0:\n",
    "                    raise RuntimeError('Failed to change ' + f + ' image, step ' + str(i))\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",
    "            os.system('cd ' + tdir + ' ; fossil close -f')\n",
    "            os.rmdir(tdir)\n",
    "        if os.path.exists(repo): os.remove(repo)    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%config InlineBackend.figure_formats = ['svg']\n",
    "\n",
    "import matplotlib as mpl\n",
    "import matplotlib.pyplot as plt\n",
    "\n",
    "data = pd.concat(repo_sizes, axis=1)\n",
    "mpl.rcParams['figure.figsize'] = (7, 4)\n",
    "plt.rcParams['axes.facecolor'] = 'white'\n",
    "data.plot(kind = 'bar', colormap = 'coolwarm',\n",
    "          grid = False, width = 0.8,\n",
    "          edgecolor = 'white', linewidth = 2)\n",
    "plt.savefig('image-format-vs-repo-size.svg')\n",
    "plt.show()"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 2",
   "language": "python",
   "name": "python2"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 2
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython2",
   "version": "2.7.15"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}

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# Image Format vs Fossil Repo Size

## The Problem

Fossil has a [delta compression][dc] feature which removes redundant
information from a file when checking in a subsequent version.¹ That
delta is then [zlib][zl]-compressed before being stored in the Fossil
repository database file.

These two steps have a few practical consequences when it comes to
storing already-compressed files:

1.  Binary data compression algorithms such as zlib turn the file data
    into [pseudorandom noise][prn].  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
    pathalogical 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.

[dc]:  ./delta_format.wiki
[hf]:  https://en.wikipedia.org/wiki/Hash_function
[prn]: https://en.wikipedia.org/wiki/Pseudorandomness
[zl]:  http://www.zlib.net/


## Key Advice

If you read no further, the takeaway from the prior two points is that
you should not store already-compressed data in a Fossil repository.
You’ll defeat both of its compression methods, ballooning the Fossil
repository size.

The remainder of this article shows the consequences of ignoring this
advice. We’ll use 2D image files as our example here, but realize that
this advice also applies to many other file types:

*   **Microsoft Office**: The [XML-based document formats][oox] used
    from Office 2003 onward (`.docx`, `.xlsx`, `.pptx`, etc.) are Zip
    files containing an XML document file and several collateral files.
    The same is true of LibreOffice’s [ODF][odf] files.

*   **[Java][jcl]**: A `.jar` file is a Zip file containing JVM
    `.class` files, manifest files, and more.

*   **[Windows Installer][wi]:** An `*.msi` file is a proprietary
    database format that contains, among other things, [Microsoft
    Cabinet][cab]-compressed files, which in turn may hold Windows
    executables, which [may themselves be compressed][exc].

*   **SVG, PDF**: Many file formats are available in both compressed
    and uncompressed forms. For the same basic reason as we will
    illustrate below, you should use the uncompressed form with Fossil
    wherever practical.


[cab]: https://en.wikipedia.org/wiki/Cabinet_(file_format)
[exc]: https://en.wikipedia.org/wiki/Executable_compression
[jcl]: https://en.wikipedia.org/wiki/Java_(programming_language)
[odf]: https://en.wikipedia.org/wiki/OpenDocument
[oox]: https://en.wikipedia.org/wiki/Office_Open_XML
[wi]:  https://en.wikipedia.org/wiki/Windows_Installer



## Demonstration

The [`image-format-vs-repo-size.ipynb` file][nb] in this directory is a
[Jupyter][jp] notebook implementing the following experiment:

1.  Create an empty Fossil repository, and save its 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 difficult.

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,² and PNG.

7.  Create a bar chart showing how the Fossil repository size changes
    with each checkin.

We chose to use Jupyter 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 respository?  Easily done with a small amount of code.

[im]: https://www.imagemagick.org/
[jp]: https://jupyter.org/
[nb]: ./image-format-vs-repo-size.ipynb
[wp]: http://wand-py.org/


## Results

Running the notebook gives a bar chart something like³ this:

![results bar chart](./image-format-vs-repo-size.svg)

There are several points of interest in that chart:

*   The initial repository size (group "0") is the same in all four
    cases. This is the normal overhead for an empty Fossil repository,
    about 200 kiB.

*   BMP and uncompressed TIFF are nearly identical in size for all
    checkins. A low-tech format like BMP will have a small edge in
    practice because TIFF metadata includes the option for multiple
    timestamps, UUIDs, etc., which bloat the checkin size by creating
    many small deltas.  If you don't need the advantages of TIFF, a less
    capable image file format will give smaller checkin sizes for a
    given amount of change.

*   Because both PNG and Fossil use the zlib binary data compression
    algorithm, the first checkin (group “1”) is approximately the same
    size for PNG, BMP, and TIFF.

*   The repo size balloons on the first 3 checkins due to SQLite page
    overhead and such.

*   Once we’re past that initial settling-in point, the repo size goes
    up negligibly for BMP and TIFF due to Fossil’s delta compression
    algorithm: a single-pixel change results in a very small increase in
    the Fossil repo size, as we want.  PNG and JPEG, though, show large
    increases on each checkin because this same tiny input change causes
    a large change in the computed delta.

*   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 test.
    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
often make it either difficult or impossible to work with the
uncompressed form, we want an automated method for producing the
uncompressed form to make Fossil happy while still having the compressed
form to keep our content creation applications happy.  This `Makefile`
will do that for several different compressed file types:

        .SUFFIXES: .bmp .png .svg .svgz

        .svgz.svg:
            gzip -dc < $< > $@

        .svg.svgz:
            gzip -9c < $< > $@

        .bmp.png:
            convert -quality 95 $< $@

        .png.bmp:
            convert $< $@

        SS_FILES := $(wildcard spreadsheet/*)


        all: $(SS_FILES) illus.svg image.bmp doc-big.pdf

        reconstitute: illus.svgz image.png
            unzip spreadsheet.xlsx -d spreadsheet
            qpdf doc-small.pdf doc-big.pdf


        $(SS_FILES): spreadsheet.xlsx
            unzip $@ -d $<

        doc-big.pdf: doc-small.pdf
            qpdf --stream-data=uncompress $@ $<

This `Makefile` allows you to treat the compressed version as the
process input, but to actually check in only the changes against the
uncompressed version by typing “`make`” before “`fossil ci`”.

Because it’s based on dependency rules, only the necessary files are
generated on each `make` command.

You only have to run “`make reconstitute`” *once* after opening a fresh
Fossil checkout to produce those compressed sources. After that, you
work with the compressed files in your content creation programs.

The `Makefile` illustrates two primary strategies:


### Input and Ouput File Formats Differ by Extension

In the case of SVG and the bitmap image formats, the file name extension
differs between the cases, so we can use `make` suffix rules to get the
behavior we want.  The top half of the `Makefile` just tells `make` how
to map from `*.svg` to `*.svgz` and vice versa, and the same for `*.bmp`
to/from `*.png`.


### Same Extension

We don’t have that luxury for Excel and PDF files, for different
reasons:

*   **Excel:** Excel has no way to work with the unpacked Zip file
    contents at all, so we have to unpack it into a subdirectory, which
    is what we check into Fossil.  On making a fresh Fossil checkout, we
    have to pack that subdirectory’s contents back up into an `*.xlsx`
    file with “`make reconstitute`” so we can edit it with Excel again.

*   **PDF:** All PDF readers can display an uncompressed PDF file, but
    many PDF-*producing* programs have no option for uncompressed
    output.  Since the file name extension is the same either way, we
    treat the compressed PDF as the source to the process, yielding an
    automatically-uncompressed PDF for the benefit of Fossil.  Unlike
    with the Excel case, there is no simple “file base name to directory
    name” mapping, so we just created the `-big` to `-small` name scheme
    here.

----


## Footnotes

1.  Several other programs also do delta compression, so they’ll also be
    affected by this problem: [rsync][rs], [Unison][us], [Git][git],
    etc. When using file copying and synchronization programs *without*
    delta compression, 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.  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.

3.  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 experient][mce].  We’ve found that
    the overall character of the results don’t change much from one run
    to the next.

[git]: https://git-scm.com/
[lzw]: https://en.wikipedia.org/wiki/Lempel%E2%80%93Ziv%E2%80%93Welch
[rs]:  https://rsync.samba.org/
[us]:  http://www.cis.upenn.edu/~bcpierce/unison/

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