I just gave a talk about this at SCaLE 17x. Here are the video of the talk and the “slides”.
Vnlog (“vanilla-log”) is a toolkit for manipulating tabular ASCII data with
labelled fields using normal UNIX tools. If you regularly use awk and sort
and uniq and others, these tools will make you infinitely more powerful. The
vnlog tools extend, rather than replace the standard tooling, so minimal
effort is required to learn and use these tools.
Everything assumes a trivially simple log format:
- A whitespace-separated table of ASCII human-readable text
- A
#character starts a comment that runs to the end of the line (like in many scripting languages) - The first line that begins with a single
#(not##or#!) is a legend, naming each column. This is required, and the field names that appear here are referenced by all the tools. - Empty fields reported as
-
This describes 99% of the format, with some extra details below. Example:
#!/usr/bin/whatever # a b c 1 2 3 ## comment 4 5 6
Such data can be processed directly with almost any existing tool, and this toolkit allows the user to manipulate this data in a nicer way by relying on standard UNIX tools. The core philosophy is to avoid creating new knowledge as much as possible. Consequently, the vnlog toolkit relies heavily on existing (and familiar!) tools and workflows. As such, the toolkit is small, light, and has a very friendly learning curve.
I have two sets of historical stock data, from the start of 2018 until now (2018/11):
< dji.vnl head -n 4# Date Open High Low Close AdjClose Volume 2018-11-15 25061.48 25354.56 24787.79 25289.27 25289.27 383292840 2018-11-14 25388.08 25501.29 24935.82 25080.50 25080.50 384240000 2018-11-13 25321.21 25511.03 25193.78 25286.49 25286.49 339690000
And
< tsla.vnl head -n 4# Date Open High Low Close AdjClose Volume 2018-11-15 342.33 348.58 339.04 348.44 348.44 4486339 2018-11-14 342.70 347.11 337.15 344.00 344.00 5036300 2018-11-13 333.16 344.70 332.20 338.73 338.73 5448600
I can add whitespace to make the headers more legible by humans:
< dji.vnl head -n 4 | vnl-align# Date Open High Low Close AdjClose Volume 2018-11-15 25061.48 25354.56 24787.79 25289.27 25289.27 383292840 2018-11-14 25388.08 25501.29 24935.82 25080.50 25080.50 384240000 2018-11-13 25321.21 25511.03 25193.78 25286.49 25286.49 339690000
I can pull out the closing prices:
< dji.vnl vnl-filter -p Close | head -n4# Close 25289.27 25080.50 25286.49
vnl-filter is primarily a wrapper around awk or perl, allowing the user to
reference columns by name. I can then plot the closing prices:
< dji.vnl vnl-filter -p Close |
feedgnuplot --lines --unset grid
Here I kept only the closing price column, so the x-axis is just the row index. The data was in reverse chronological order, so this plot is also in reverse chronological order. Let’s fix that:
< dji.vnl vnl-sort -k Date |
vnl-filter -p Close |
feedgnuplot --lines --unset grid
The vnl-sort tool (and most of the other vnl-xxx tools) are wrappers around
the core tools already available on the system (such as sort, in this case).
With the primary difference being reading/writing vnlog, and referring to
columns by name.
We now have the data in the correct order, but it’d be nice to see the actual dates on the x-axis. While we’re at it, let’s label the axes too:
< dji.vnl vnl-filter -p Date,Close | head -n4# Date Close 2018-11-15 25289.27 2018-11-14 25080.50 2018-11-13 25286.49
< dji.vnl vnl-sort -k Date |
vnl-filter -p Date,Close |
feedgnuplot --lines --unset grid --timefmt %Y-%m-%d --domain \
--xlabel 'Date' --ylabel 'Price ($)'
What was the highest value of the Dow-Jones index, and when did it happen?
< dji.vnl vnl-sort -rgk Close |
head -n2 |
vnl-align# Date Open High Low Close AdjClose Volume 2018-10-03 26833.47 26951.81 26789.08 26828.39 26828.39 280130000
Alrighty. Looks like the high was in October. Let’s zoom in on that month:
< dji.vnl vnl-sort -k Date |
vnl-filter 'Date ~ /2018-10/' -p Date,Close |
feedgnuplot --lines --unset grid --timefmt %Y-%m-%d --domain \
--xlabel 'Date' --ylabel 'Price ($)'
OK. Is this thing volatile? What was the largest single-day gain?
< dji.vnl vnl-filter -p '.,d=diff(Close)' |
head -n4 |
vnl-align# Date Open High Low Close AdjClose Volume d 2018-11-15 25061.48 25354.56 24787.79 25289.27 25289.27 383292840 - 2018-11-14 25388.08 25501.29 24935.82 25080.50 25080.50 384240000 -208.77 2018-11-13 25321.21 25511.03 25193.78 25286.49 25286.49 339690000 205.99
< dji.vnl vnl-filter -p '.,d=diff(Close)' |
vnl-sort -rgk d |
head -n2 |
vnl-align# Date Open High Low Close AdjClose Volume d 2018-02-02 26061.79 26061.79 25490.66 25520.96 25520.96 522880000 1175.21
Whoa. So the best single-gain day was 2018-02-02: the dow gained 1175.21 points between closing on Feb 1 and Feb 2. But it actually lost ground that day! What if I looked at the difference between the opening and closing in a single day?
< dji.vnl vnl-filter -p '.,d=Close-Open' |
vnl-sort -rgk d |
head -n2 |
vnl-align# Date Open High Low Close AdjClose Volume d 2018-02-06 24085.17 24946.23 23778.74 24912.77 24912.77 823940000 827.6
I guess by that metric 2018-02-06 was better. Let’s join the Dow-jones index data and the TSLA data, and let’s look at them together:
vnl-join --vnl-autosuffix dji.vnl tsla.vnl -j Date |
head -n4 |
vnl-align# Date Open_dji High_dji Low_dji Close_dji AdjClose_dji Volume_dji Open_tsla High_tsla Low_tsla Close_tsla AdjClose_tsla Volume_tsla 2018-11-15 25061.48 25354.56 24787.79 25289.27 25289.27 383292840 342.33 348.58 339.04 348.44 348.44 4486339 2018-11-14 25388.08 25501.29 24935.82 25080.50 25080.50 384240000 342.70 347.11 337.15 344.00 344.00 5036300 2018-11-13 25321.21 25511.03 25193.78 25286.49 25286.49 339690000 333.16 344.70 332.20 338.73 338.73 5448600
vnl-join --vnl-autosuffix dji.vnl tsla.vnl -j Date |
vnl-filter -p '^Close' |
head -n4 |
vnl-align# Close_dji Close_tsla 25289.27 348.44 25080.50 344.00 25286.49 338.73
vnl-join --vnl-autosuffix dji.vnl tsla.vnl -j Date |
vnl-filter -p '^Close' |
feedgnuplot --domain --points --unset grid \
--xlabel 'DJI price ($)' --ylabel 'TSLA price ($)'
Huh. Apparently there’s no obvious, strong correlation between TSLA and Dow-Jones closing prices. And we saw that with just a few shell commands, without dropping down into a dedicated analysis system.
vnlog is a part of Debian/buster and Ubuntu/cosmic (18.10) and later. On those boxes you can simply
$ sudo apt install vnlog libvnlog-dev libvnlog-perl python3-vnlog
to get the binary tools, the C API, the perl and python3 interfaces respectively.
Most of this is written in an interpreted language, so there’s nothing to build or install, and you can run the tools directly from the source tree:
$ git clone https://github.com/dkogan/vnlog.git $ cd vnlog $ ./vnl-filter .....
The python and perl libraries can be run from the tree by setting the
PYTHONPATH and PERL5LIB environment variables respectively. For the C
library, you should make, and then point your CFLAGS and LDLIBS and
LD_LIBRARY_PATH to the local tree.
If you do want to install to some arbitrary location to simplify the paths, do this:
$ make $ PREFIX=/usr/local make install
This will install all the components into /usr/local.
Vnlog data is nicely readable by both humans and machines. Any time your
application invokes printf() for either diagnostics or logging, consider
writing out vnlog-formatted data. You retain human readability, but gain the
power all the vnl-... tools provide.
Vnlog tools are designed to be very simple and light. There’s an ever-growing list of other tools that do vaguely the same thing. Some of these:
- https://github.com/BurntSushi/xsv
- https://csvkit.readthedocs.io/
- https://github.com/johnkerl/miller
- https://github.com/jqnatividad/qsv
- https://github.com/greymd/teip
- https://github.com/eBay/tsv-utils-dlang
- https://www.gnu.org/software/datamash/
- https://stedolan.github.io/jq/
- https://github.com/benbernard/RecordStream
- https://github.com/dinedal/textql
- https://www.visidata.org/
- http://harelba.github.io/q/
- https://github.com/BatchLabs/charlatan
- https://github.com/dbohdan/sqawk
Many of these provide facilities to run various analyses, and others focus on data types that aren’t just a table (json for instance). Vnlog by contrast doesn’t analyze anything, and targets the most trivial possible data format. This makes it very easy to run any analysis you like in any tool you like. The main envisioned use case is one-liners, and the tools are geared for that purpose. The above mentioned tools are much more powerful than vnlog, so they could be a better fit for some use cases. I claim that
- 90% of the time you want to do simple things, and vnlog is a great fit for the task
- If you really do need to do something complex, you shouldn’t be in the shell writing oneliners anymore, and a fully-fledged analysis system (numpy, etc) is more appropriate
In the spirit of doing as little as possible, the provided tools are wrappers around tools you already have and are familiar with. The provided tools are:
vnl-filteris a tool to select a subset of the rows/columns in a vnlog and/or to manipulate the contents. This is anawkwrapper where the fields can be referenced by name instead of index. 20-second tutorial:
vnl-filter -p col1,col2,colx=col3+col4 'col5 > 10' --has col6will read the input, and produce a vnlog with 3 columns: col1 and col2
from the input, and a column colx that’s the sum of col3 and col4 in the
input. Only those rows for which both col5 > 10 is true and that have a
non-null value for col6 will be output. A null entry is signified by a
single - character.
vnl-filter --eval '{s += x} END {print s}'will evaluate the given awk program on the input, but the column names work as
you would hope they do: if the input has a column named x, this would
produce the sum of all values in this column.
vnl-sort,vnl-uniq,vnl-join,vnl-tail,vnl-tsare wrappers around the corresponding commandline tools. These work exactly as you would expect also: the columns can be referenced by name, and the legend comment is handled properly. These are wrappers, so all the commandline options those tools have “just work” (except options that don’t make sense in the context of vnlog). As an example,vnl-tail -fwill follow a log: data will be read byvnl-tailas it is written into the log (just liketail -f, but handling the legend properly). And you already know how to use these tools without even reading the manpages! Note: I use the Linux kernel and the tools from GNU Coreutils exclusively, but this all has been successfully tested on FreeBSD and OSX also. Please let me know if something doesn’t work.vnl-alignaligns vnlog columns for easy interpretation by humans. The meaning is unaffectedVnlog::Parseris a simple perl library to read a vnlogvnlogis a simple python library to read a vnlog. Both python2 and python3 are supportedlibvnlogis a C library to simplify reading and writing a vnlog. Clearly all you really need for writing isprintf(), but this is useful if we have lots of columns, many containing null values in any given row, and/or if we have parallel threads writing to a log. In my usage I have hundreds of columns of sparse data, so this is handyvnl-make-matrixconverts a one-point-per-line vnlog to a matrix of data. I.e.
$ cat dat.vnl # i j x 0 0 1 0 1 2 0 2 3 1 0 4 1 1 5 1 2 6 2 0 7 2 1 8 2 2 9 3 0 10 3 1 11 3 2 12 $ < dat.vnl vnl-filter -p i,x | vnl-make-matrix --outdir /tmp Writing to '/tmp/x.matrix' $ cat /tmp/x.matrix 1 2 3 4 5 6 7 8 9 10 11 12
All the tools have manpages that contain more detail. And more tools will probably be added with time.
The high-level description of the vnlog format from above is sufficient to read/write “normal” vnlog data, but there are a few corner cases that should be mentioned. To reiterate, the format description from above describes vnlog as:
- A whitespace-separated table of ASCII human-readable text
- A
#character starts a comment that runs to the end of the line (like in many scripting languages) - The first line that begins with a single
#(not##or#!) is a legend, naming each column. This is required, and the field names that appear here are referenced by all the tools. - Empty fields reported as
-
For a few years now I’ve been using these tools myself, and supporting others as they were passing vnlog data around. In the process I’ve encountered some slightly-weird data, and patched the tools to accept it. So today the included vnlog tools are very permissive, and accept any vnlog data that can possibly be accepted. Other vnlog tools may not be quite as permissive, and may not be able to interpret “weird” data. Points of note, describing the included vnlog tools:
- Leading and trailing whitespace is ignored. Everywhere. So this data file will
be read properly, with the
xcolumn containing 1 and 3:# x y 1 2 3 4 - Empty (or whitespace-only) lines anywhere are ignored, and treated as a comment
- An initial
#comment without field names is treated as a comment, and we continue looking for the legend in the following lines. So this data file will be read properly:## comment # # x y 1 2 3 4 - Trailing comments are supported, like in most scripting languages. So this
data file will be read properly:
# x y 1 2 # comment 3 4 - Field names are very permissive: anything that isn’t whitespace is
supported. So this data file will be read properly:
# x y # 1+ - 1 2 3 4 5 11 12 13 14 15We can pull out the
#and1+and-columns:vnl-filter -p '#,1+,-'And we can even operate on them, if we use whitespace to indicate field boundaries:
vnl-filter -p 'x=1+ + 5'Note that this implies that trailing comments in a legend line are not supported: the extra
#characters will be used for field names. Field names containing,or === are currently not accepted byvnl-filter, but are accepted by the other tools (vnl-sortand such). I’ll makevnl-filterable to work with those field names too, eventually, but as a user, the simplest thing to do is to not pass around data with such field names. - Duplicated labels are supported whenever possible. So
# x y z z 1 2 3 4 11 12 13 14will work just fine, unless we’re operating on
z. With this data, both of these commands work:vnl-filter -p x vnl-filter -p zPicking
zselects both of thezcolumns. But neither of these commands can work with the non-uniquezcolumn:vnl-filter -p s=z+1 vnl-sort -k z
A common use case is a complex application that produces several semi-related subsets of data at once. Example: a moving vehicle is reporting both its own position and the observed positions of other vehicles; at any given time any number of other vehicles may be observed. Two equivalent workflows are possible:
- a single unified vnlog stream for all the data
- several discrete vnlog streams for each data subset
Both are valid approaches
Here the application produces a single vnlog that contains all the columns,
from all the data subsets. In any given row, many of the columns will be empty
(i.e. contain only - ). For instance, a row describing a vehicle own position
will not have data about any observations, and vice versa. It is inefficient to
store all the extra - but it makes many things much nicer, so it’s often worth
it. vnl-filter can be used to pull out the different subsets. Sample
joint.vnl:
# time x_self x_observation 1 10 - 2 20 - 2 - 100 3 30 - 3 - 200 3 - 300
Here we have 3 instances in time. We have no observations at time 1, one
observation at time 2, and two observations at time 3. We can use
vnl-filter to pull out the data we want:
$ < joint.vnl vnl-filter -p time,self # time x_self 1 10 2 20 2 - 3 30 3 - 3 -
If we only care about our own positions, the + modifier in picked columns in
vnl-filter is very useful here:
$ < joint.vnl vnl-filter -p time,+self # time x_self 1 10 2 20 3 30 $ < joint.vnl vnl-filter -p time,+observation # time x_observation 2 100 3 200 3 300
Note that the default is --skipempty, so if we’re only looking at x_self
for instance, then we don’t even need to + modifier:
$ < joint.vnl vnl-filter -p self # x_self 10 20 30
Also, note that the vnlog C interface works very nicely to produce these
datafiles:
- You can define lots and lots of columns, but only fill some of them before
calling
vnlog_emit_record(). The rest will be set to-. - You can create multiple contexts for each type of data, and you can populate
them with data independently. And when calling
vnlog_emit_record_ctx(), you’ll get a record with data for just that context.
Conversely, the application can produce separate vnlog streams for each
subset of data. Depending on what is desired, exactly, vnl-join can be used to
re-join them:
$ cat self.vnl # time x_self 1 10 2 20 3 30 $ cat observations.vnl # time x_observation 2 100 3 200 3 300 $ vnl-join -j time -a- self.vnl observations.vnl # time x_self x_observation 1 10 - 2 20 100 3 30 200 3 30 300
A common need is to compute basic statistics from your data. Many of the
alternative toolkits listed above provide built-in facilities to do this, but
vnlog does not: it’s meant to be unixy, where each tool has very limited scope.
Thus you can either do this with awk like you would normally, or you can use
other standalone tools to perform the needed computations. For instance, I can
generate some data:
$ seq 2 100 | awk 'BEGIN {print "# x"} {print log($1)}' > /tmp/log.vnl
Then I can compute the mean with awk:
$ < /tmp/log.vnl vnl-filter --eval '{sum += x} END {print sum/NR}'
3.67414
Or I can compute the mean (and other stuff) with a separate standalone tool:
$ < /tmp/log.vnl ministat
x <stdin>
+----------------------------------------------------------------------------+
| xx |
| x xxxxxxx |
| xx xxxxxxxxxxxx|
| x x xxxxxxxxxxxxxxxxxxxxxxx|
|x x x x x x x x x xx xx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx|
| |_______________A____M___________| |
+----------------------------------------------------------------------------+
N Min Max Median Avg Stddev
x 99 0.693147 4.60517 3.93183 3.6741353 0.85656382
ministat is not a part of the vnlog toolkit, but the vnlog format is generic
so it works just fine.
Everything about vnlog is generic and simple, so it’s easy to use it to process
data that wasn’t originally meant to be used this way. For instance filtering
the output of ls -l to report only file names and sizes, skipping directories,
and sorting by file sizes:
$ ls -l total 320 -rw-r--r-- 1 dima dima 5044 Aug 25 15:04 Changes -rw-r--r-- 1 dima dima 12749 Aug 25 15:04 Makefile -rw-r--r-- 1 dima dima 69789 Aug 25 15:04 README.org -rw-r--r-- 1 dima dima 33781 Aug 25 15:04 README.template.org -rw-r--r-- 1 dima dima 5359 Aug 25 15:04 b64_cencode.c drwxr-xr-x 4 dima dima 4096 Aug 25 15:04 completions drwxr-xr-x 3 dima dima 4096 Aug 25 15:04 lib drwxr-xr-x 3 dima dima 4096 Aug 25 15:04 packaging drwxr-xr-x 2 dima dima 4096 Aug 25 15:04 test -rwxr-xr-x 1 dima dima 5008 Aug 25 15:04 vnl-align -rwxr-xr-x 1 dima dima 56637 Aug 25 15:04 vnl-filter -rwxr-xr-x 1 dima dima 5678 Aug 25 15:04 vnl-gen-header -rwxr-xr-x 1 dima dima 29815 Aug 25 15:04 vnl-join -rwxr-xr-x 1 dima dima 3631 Aug 25 15:04 vnl-make-matrix -rwxr-xr-x 1 dima dima 8372 Aug 25 15:04 vnl-sort -rwxr-xr-x 1 dima dima 5822 Aug 25 15:04 vnl-tail -rwxr-xr-x 1 dima dima 4439 Aug 25 15:04 vnl-ts -rw-r--r-- 1 dima dima 559 Aug 25 15:04 vnlog-base64.h -rw-r--r-- 1 dima dima 8169 Aug 25 15:04 vnlog.c -rw-r--r-- 1 dima dima 12677 Aug 25 15:04 vnlog.h $ (echo '# permissions num_links user group size month day time name'; ls -l | tail -n +2) | vnl-filter 'permissions !~ "^d"' -p name,size | vnl-sort -gk size | vnl-align # name size vnlog-base64.h 559 vnl-make-matrix 3631 vnl-ts 4439 vnl-align 5008 Changes 5044 b64_cencode.c 5359 vnl-gen-header 5678 vnl-tail 5822 vnlog.c 8169 vnl-sort 8372 vnlog.h 12677 Makefile 12749 vnl-join 29815 README.template.org 33781 vnl-filter 56637 README.org 69789
With a bit of shell manipulation, these tools can be applied to a whole lot of different data streams that know nothing of vnlog.
For most uses, vnlog files are simple enough to be generated with plain prints. But then each print statement has to know which numeric column we’re populating, which becomes effortful with many columns. In my usage it’s common to have a large parallelized C program that’s writing logs with hundreds of columns where any one record would contain only a subset of the columns. In such a case, it’s helpful to have a library that can output the log files. This is available. Basic usage looks like this:
In a shell:
vnl-gen-header 'int w' 'uint8_t x' 'char* y' 'double z' 'void* binary' > vnlog_fields_generated.hIn a C program test.c:
#include "vnlog_fields_generated.h"
int main()
{
vnlog_emit_legend();
vnlog_set_field_value__w(-10);
vnlog_set_field_value__x(40);
vnlog_set_field_value__y("asdf");
vnlog_emit_record();
vnlog_set_field_value__z(0.3);
vnlog_set_field_value__x(50);
vnlog_set_field_value__w(-20);
vnlog_set_field_value__binary("\x01\x02\x03", 3);
vnlog_emit_record();
vnlog_set_field_value__w(-30);
vnlog_set_field_value__x(10);
vnlog_set_field_value__y("whoa");
vnlog_set_field_value__z(0.5);
vnlog_emit_record();
return 0;
}Then we build and run, and we get
$ cc -o test test.c -lvnlog $ ./test # w x y z binary -10 40 asdf - - -20 50 - 0.2999999999999999889 AQID -30 10 whoa 0.5 -
The binary field in base64-encoded. This is a rarely-used feature, but sometimes you really need to log binary data for later processing, and this makes it possible.
So you
- Generate the header to define your columns
- Call
vnlog_emit_legend() - Call
vnlog_set_field_value__...()for each field you want to set in that row. - Call
vnlog_emit_record()to write the row and to reset all fields for the next row. Any fields unset with avnlog_set_field_value__...()call are written as null:-
This is enough for 99% of the use cases. Things get a bit more complex if we have have threading or if we have multiple vnlog ouput streams in the same program. For both of these we use vnlog contexts.
To support independent writing into the same vnlog (possibly by multiple threads; this is reentrant), each log-writer should create a context, and use it when talking to vnlog. The context functions will make sure that the fields in each context are independent and that the output records won’t clobber each other:
void child_writer( // the parent context also writes to this vnlog. Pass NULL to
// use the global one
struct vnlog_context_t* ctx_parent )
{
struct vnlog_context_t ctx;
vnlog_init_child_ctx(&ctx, ctx_parent);
while(records)
{
vnlog_set_field_value_ctx__xxx(&ctx, ...);
vnlog_set_field_value_ctx__yyy(&ctx, ...);
vnlog_set_field_value_ctx__zzz(&ctx, ...);
vnlog_emit_record_ctx(&ctx);
}
vnlog_free_ctx(&ctx); // required only if we have any binary fields
}If we want to have multiple independent vnlog writers to different streams (with different columns and legends), we do this instead:
file1.c:
#include "vnlog_fields_generated1.h"
void f(void)
{
// Write some data out to the default context and default output (STDOUT)
vnlog_emit_legend();
...
vnlog_set_field_value__xxx(...);
vnlog_set_field_value__yyy(...);
...
vnlog_emit_record();
}file2.c:
#include "vnlog_fields_generated2.h"
void g(void)
{
// Make a new session context, send output to a different file, write
// out legend, and send out the data
struct vnlog_context_t ctx;
vnlog_init_session_ctx(&ctx);
FILE* fp = fopen(...);
vnlog_set_output_FILE(&ctx, fp);
vnlog_emit_legend_ctx(&ctx);
...
vnlog_set_field_value__a(...);
vnlog_set_field_value__b(...);
...
vnlog_free_ctx(&ctx); // required only if we have any binary fields
vnlog_emit_record();
}Note that it’s the user’s responsibility to make sure the new sessions go to a
different FILE by invoking vnlog_set_output_FILE(). Furthermore, note that
the included vnlog_fields_....h file defines the fields we’re writing to; and
if we have multiple different vnlog field definitions in the same program (as in
this example), then the different writers must live in different source files.
The compiler will barf if you try to #include two different
vnlog_fields_....h files in the same source.
vnlog_printf(...)andvnlog_printf_ctx(ctx, ...)write to a pipe like
printf() does. This exists primarily for comments.
vnlog_clear_fields_ctx(ctx, do_free_binary)clears out the data in a context
and makes it ready to be used for the next record. It is rare for the user to have to call this manually. The most common case is handled automatically (clearing out a context after emitting a record). One area where this is useful is when making a copy of a context:
struct vnlog_context_t ctx1;
// .... do stuff with ctx1 ... add data to it ...
struct vnlog_context_t ctx2 = ctx1;
// ctx1 and ctx2 now both have the same data, and the same pointers to
// binary data. I need to get rid of the pointer references in ctx1
vnlog_clear_fields_ctx(&ctx1, false);vnlog_free_ctx(ctx)frees memory for an vnlog context. Do this before
throwing the context away. Currently this is only needed for context that have binary fields, but this should be called for all contexts anyway, in case this changes in a later revision
The basic usage goes like this:
#include <stdio.h>
#include <stdbool.h>
#include <vnlog/vnlog-parser.h>
bool parse_vnlog(const char* filename)
{
FILE* fp = fopen(filename);
if(fp == NULL)
return false;
vnlog_parser_t ctx;
if(VNL_OK != vnlog_parser_init(&ctx, fp))
return false;
// String in the "time" column for the most-recently-parsed row
const char*const* time_record = vnlog_parser_record_from_key(&ctx, "time");
if(time_record == NULL)
{
vnlog_parser_free(&ctx);
return false;
}
int i_record = 0;
vnlog_parser_result_t result;
while(VNL_OK == (result = vnlog_parser_read_record(&ctx, fp)))
{
for(int i=0; i<ctx.Ncolumns; i++)
printf("Record %d: %s = %s\n",
i_record,
ctx.record[i].key, ctx.record[i].value);
printf("Record %d: time = %s\n",
i_record, *time_record);
i_record++;
}
vnlog_parser_free(&ctx);
return true;
}The usage should be clear from this example. See vnlog-parser.h for details.
The C interface supports writing base64-encoded binary data using Chris Venter’s
libb64. The base64-encoder used here was slightly modified: the output appears
all on one line, making is suitable to appear in a vnlog field. If we’re writing
a vnlog with printf() directly without using the vnlog.h interface described
above, we allow this modified base64 encoder to be invoked by itself. Usage:
void* binary_buffer = ...;
int binary_buffer_len = ...;
char base64_buffer[vnlog_base64_dstlen_to_encode(binary_buffer_len)];
vnlog_base64_encode( base64_buffer, sizeof(base64_buffer),
binary_buffer, binary_buffer_len );Clearly the above example allocates the base64 buffer on the stack, so it’s only suitable for small-ish data chunks. But if you have lots and lots of data, probably writing it as base64 into a vnlog isn’t the best thing to do.
Reading vnlog data into a python program is simple. The vnlog Python module
provides three different ways to do that:
- slurp the whole thing into a numpy array using the
slurp()function. Basic usage:import vnlog arr,list_keys,dict_key_index = \ vnlog.slurp(filename_or_fileobject)
This parses out the legend, and then calls
numpy.loadtxt(). Null data values (-) are not supported - Iterate through the records:
vnlogclass, used as an iterator. Basic usage:import vnlog for d in vnlog.vnlog(filename_or_fileobject): print(d['time'],d['height'])
Null data values are represented as
None - Parse incoming lines individually:
vnlogclass, using theparse()method. Basic usage:import vnlog parser = vnlog.vnlog() for l in file: parser.parse(l) d = parser.values_dict() if not d: continue print(d['time'],d['height'])
Most of the time you’d use options 1 or 2 above. Option 3 is the most general, but also the most verbose and slowest.
The slurp() example from above is simple: it doesn’t specify a dtype (data
type), so float (64-bit IEEE-754 float) is used by default, for all the data
in the array. You can specify another dtype, for instance:
arr,list_keys,dict_key_index = \
vnlog.slurp(filename_or_fileobject,
dtype = int)You can also specify a /structured/ dtype to pull out different columns, with different individual dtypes. Most notably, this allows interpreting some columns as strings. Let’s say you have a very common vnlog data, such as this “data.vnl”:
# image x y z temperature image1.png 1 2 5 34 image2.png 3 4 1 35
Reading this with a simple vnlog.slurp() will fail: the filenames are not
parseable as numerical values. We can instead do this:
dtype = np.dtype([ ('image', 'U16'),
('x y z', int, (3,)),
('temperature', float), ])
arr = vnlog.slurp("data.vnl", dtype=dtype)This will read the image filename, the xyz points and the temperature into different sub-arrays, with different types each. Accessing the result looks like this:
print(arr['image'])
---> array(['image1.png', 'image2.png'], dtype='<U16')
print(arr['x y z'])
---> array([[1, 2, 5],
[3, 4, 1]])
print(arr['temperature'])
---> array([34., 35.])
Notes:
- The given structured dtype defines both how to organize the data, and which data to extract. So it can be used to read in only a subset of the available columns. Here I could have omitted the ‘temperature’ column, for instance
- Sub-arrays are allowed. In the example I could say either
dtype = np.dtype([ ('image', 'U16'), ('x y z', int, (3,)), ('temperature', float), ])
or
dtype = np.dtype([ ('image', 'U16'), ('x', int), ('y', int), ('z', int), ('temperature', float), ])
The latter would read
x,y,zinto separate, individual arrays. Sometime we want this, sometimes not. - Nested structured dtypes are not allowed. Fields inside other fields are not supported, since it’s not clear how to map that to a flat vnlog legend
- If a structured dtype is given,
slurp()returns the array only, since the field names are already available in the dtype
If we need to read data into numpy specifically, nicer tools are available than
the generic vnlog Python module. The built-in numpy.loadtxt numpy.savetxt
functions work well (with the caveat that numpy.loadtxt() should be followed
by numpysane.atleast_dims(..., -2) to make sure that a data array of shape
(Nrows,Ncols) is returned even if Nrows==1. For example to write to standard
output a vnlog with fields a, b and c:
numpy.savetxt(sys.stdout, array, fmt="%g", header="a b c")Note that numpy automatically adds the # to the header. To read a vnlog from a
file on disk, do something like
array = numpysane.atleast_dims(numpy.loadtxt('data.vnl'), -2)These functions know that # lines are comments, but don’t interpret anything
as field headers. That’s easy to do, so I’m not providing any helper libraries.
I might do that at some point, but in the meantime, patches are welcome.
I use GNU/Linux-based systems exclusively, but everything has been tested functional on FreeBSD and OSX in addition to Debian, Ubuntu and CentOS. I can imagine there’s something I missed when testing on non-Linux systems, so please let me know if you find any issues.
These tools are meant to be simple, so some things are hard requirements. A big one is that columns are whitespace-separated. There is no mechanism for escaping or quoting whitespace into a single field. I think supporting something like that is more trouble than it’s worth.
xxx-manpage-vnl-filter-xxx
xxx-manpage-vnl-align-xxx
xxx-manpage-vnl-sort-xxx
xxx-manpage-vnl-join-xxx
xxx-manpage-vnl-tail-xxx
xxx-manpage-vnl-ts-xxx
xxx-manpage-vnl-uniq-xxx
xxx-manpage-vnl-gen-header-xxx
xxx-manpage-vnl-make-matrix-xxx
https://github.com/dkogan/vnlog/
Dima Kogan ([email protected]) wrote this toolkit for his work at the Jet
Propulsion Laboratory, and is delighted to have been able to release it
publically
Chris Venter ([email protected]) wrote the base64 encoder
This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
Copyright 2016-2017 California Institute of Technology
Copyright 2017-2018 Dima Kogan ([email protected])
b64_cencode.c comes from cencode.c in the libb64 project. It is written by
Chris Venter ([email protected]) who placed it in the public domain. The
full text of the license is in that file.