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.
NAME
vnl-filter - filters vnlogs to select particular rows, fields
SYNOPSIS
$ cat run.vnl
# time x y z temperature
3 1 2.3 4.8 30
4 1.1 2.2 4.7 31
6 1 2.0 4.0 35
7 1 1.6 3.1 42
$ <run.vnl vnl-filter -p x,y,z | vnl-align
# x y z
1 2.3 4.8
1.1 2.2 4.7
1 2.0 4.0
1 1.6 3.1
$ <run.vnl vnl-filter -p i=NR,time,'dist=sqrt(x*x + y*y + z*z)' | vnl-align
# i time dist
1 3 5.41572
2 4 5.30471
3 6 4.58258
4 7 3.62905
$ <run.vnl vnl-filter 'temperature >= 35' | vnl-align
# time x y z temperature
6 1 2.0 4.0 35
7 1 1.6 3.1 42
$ <run.vnl vnl-filter --eval '{s += temperature} END { print "mean temp: " s/NR}'
mean temp: 34.5
$ <run.vnl vnl-filter -p x,y | feedgnuplot --terminal 'dumb 80,30' --unset grid --domain --lines --exit
2.3 +---------------------------------------------------------------------+
| + + *************** + |
| ************** |
| *******|
2.2 |-+ ************|
| ******** |
| ******** |
2.1 |-+ ********* +-|
| ******** |
| ******** |
| **** |
2 |-+ * +-|
| * |
| * |
| * |
1.9 |-+ * +-|
| * |
| * |
| * |
1.8 |-+ * +-|
| * |
| * |
1.7 |-+ * +-|
| * |
| * |
| * + + + + |
1.6 +---------------------------------------------------------------------+
0.98 1 1.02 1.04 1.06 1.08 1.1
DESCRIPTION
This tool is largely a frontend for awk to operate on vnlog files. Vnlog
is both an input and an output. This tool makes it very simple to select
specific rows and columns for output and to manipulate the data in
various ways.
This is a UNIX-style tool, so the input/output of this tool is strictly
STDIN/STDOUT. Furthermore, in its usual form this tool is a filter, so
the format of the output is *exactly* the same as the format of the
input. The exception to this is when using "--eval", in which the output
is dependent on whatever expression we're evaluating.
This tool is convenient to process both stored data or live data; in the
latter case, it's very useful to pipe the streaming output to
"feedgnuplot --stream" to get a realtime visualization of the incoming
data.
This tool reads enough of the input file to get a legend, at which point
it constructs an awk program to do the main work, and execs to awk (it's
possible to use perl as well, but this isn't as fast).
Input/output data format
The input/output data is vnlog: a plain-text table of values. Any lines
beginning with "#" are treated as comments, and are passed through. The
first line that begins with "#" but not "##" or "#!" is a *legend* line.
After the "#", follow whitespace-separated field names. Each subsequent
line is whitespace-separated values matching this legend. For instance,
this is a valid vnlog file:
#!/usr/bin/something
## more comments
# x y z
-0.016107 0.004362 0.005369
-0.017449 0.006711 0.006711
-0.018456 0.014093 0.006711
-0.017449 0.018791 0.006376
"vnl-filter" uses this format for both the input and the output. The
comments are preserved, but the legend is updated to reflect the fields
in the output file.
A string "-" is used to indicate an undefined value, so this is also a
valid vnlog file:
# x y z
1 2 3
4 - 6
- - 7
Filtering
To select specific *columns*, pass their names to the "-p" option (short
for "--print" or "--pick", which are synonyms). In its simplest form, to
grab only columns "x" and "y", do
vnl-filter -p x,y
See the detailed description of "-p" below for more detail.
To select specific *rows*, we use *matches* expressions. Anything on the
"vnl-filter" commandline and not attached to any "--xxx" option is such
an expression. For instance
vnl-filter 'size > 10'
would select only those rows whose "size" column contains a value > 10.
See the detailed description of matches expressions below for more
detail.
Context lines
"vnl-filter" supports the context output options ("-A", "-B" and "-C")
exactly like the "grep" tool. I.e to print out all rows whose "size"
column contains a value > 10 *but also* include the 3 rows immediately
before *and* after such matching rows, do this:
vnl-filter -C3 'size > 10'
"-B" reports the rows *before* matching ones and "-A" the rows *after*
matching ones. "-C" reports both. Note that this applies *only* to
*matches* expressions: records skipped because they fail "--has" or
"--skipempty" are *not* included in contextual output.
Backend choice
By default, the parsing of arguments and the legend happens in perl,
which then constructs a simple awk script, and invokes "mawk" to
actually read the data and to process it. This is done because awk is
lighter weight and runs faster, which is important because our data sets
could be quite large. We default to "mawk" specifically, since this is a
simpler implementation than "gawk", and runs much faster. If for
whatever reason we want to do everything with perl, this can be
requested with the "--perl" option.
Special functions
For convenience we support several special functions in any expression
passed on to awk or perl (named expressions, matches expressions,
"--eval" strings). These generally maintain some internal state, and
vnl-filter makes sure that this state is consistent. Note that these are
evaluated *after* "--skipcomments" and "--has". So any record skipped
because of a "--has" expression, for instance, will *not* be considered
in prev(), diff() and so on.
* rel(x) returns value of "x" relative to the first value of "x". For
instance we might want to see the time or position relative to the
start, not relative to some absolute beginning. Example:
$ cat tst.vnl
# time x
100 200
101 212
102 209
$ <tst.vnl vnl-filter -p 't=rel(time),x=rel(x)
# t x
0 0
1 12
2 9
* diff(x) returns the difference between the current value of "x" and
the previous value of "x". The first row will always be "-".
Example:
$ <tst.vnl vnl-filter -p x,'d1=diff(x),d2=diff(diff(x))' | vnl-align
# x d1 d2
1 - -
8 7 7
27 19 12
64 37 18
125 61 24
* sum(x) returns the cumulative sum of "x". As diff(x) can be thought
of as a derivative, sum(x) can be thought of as an integral. So
"diff(sum(x))" would return the same value as "x" (except for the
first row; diff() always returns "-" for the first row).
Example:
$ <tst.vnl vnl-filter -p 'x,s=sum(x),ds=diff(sum(x))' | vnl-align
# x s ds
1 1 -
8 9 8
27 36 27
64 100 64
125 225 125
* prev(x) returns the previous value of "x". One could construct sum()
and rel() using this, if they weren't already available.
* latestdefined(x) returns the most recent value of "x" that isn't
"-". If "x" isn't "-", this simply returns "x".
ARGUMENTS
Matches expressions
Anything on the commandline not attached to any "--xxx" option is a
*matches* expression. These are used to select particular records (rows)
in a data file. For each row, we evaluate all the expressions. If *all*
the expressions evaluate to true, that row is output. This expression is
passed directly to the awk (or perl) backend.
Example: to select all rows that have valid data in column "a" *or*
column "b" *or* column "c" you can
vnl-filter 'a != "-" || b != "-" || c != "-"'
or
vnl-filter --perl 'defined a || defined b || defined c'
As with the named expressions given to "-p" (described above), these are
passed directly to awk, so anything that can be done with awk is
supported here.
-p|--print|--pick expr
These option provide the mechanism to select specific columns for
output. For instance to pull out columns called "lat", "lon", and any
column whose name contains the string "feature_", do
vnl-filter -p lat,lon,'feature_.*'
or, equivalently
vnl-filter --print lat --print lon --print 'feature_.*'
We look for exact column name matches first, and if none are found, we
try a regex. If there was no column called exactly "feature_", then the
above would be equivalent to
vnl-filter -p lat,lon,feature_
This mechanism is much more powerful than just selecting columns. First
off, we can rename chosen fields:
vnl-filter -p w=feature_width
would pick the "feature_width" field, but the resulting column in the
output would be named "w". When renaming a column in this way regexen
are *not* supported, and exact field names must be given. But the string
to the right of the "=" is passed on directly to awk (after replacing
field names with column indices), so any awk expression can be used
here. For instance to compute the length of a vector in separate columns
"x", "y", and "z" you can do:
vnl-filter -p 'l=sqrt(x*x + y*y + z*z)'
A single column called "l" would be produced.
We can also *exclude* columns by preceding their name with "!". This
works like you expect. Rules:
* The pick/exclude directives are processed in order given to produce
the output picked-column list
* If the first "-p" item is an exclusion, we implicitly pick *all* the
columns prior to processing the "-p".
* The exclusion expressions match the *output* column names, not the
*input* names.
* We match the exact column names first. If that fails, we match as a
regex
Example. To grab all the columns *except* the temperature(s) do this:
vnl-filter -p !temperature
To grab all the columns that describe *something* about a robot (columns
whose names have the string "robot_" in them), but *not* its temperature
(i.e. *not* "robot_temperature"), do this:
vnl-filter -p robot_,!temperature
--has a,b,c,...
Used to select records (rows) that have a non-empty value in a
particular field (column). A *null* value in a column is designated with
a single "-". If we want to select only records that have a value in the
"x" column, we pass "--has x". To select records that have data for
*all* of a given set of columns, the "--has" option can be repeated, or
these multiple columns can be given in a whitespace-less comma-separated
list. For instance if we want only records that have data in *both*
columns "x" *and* "y" we can pass in "--has x,y" or "--has x --has y".
If we want to combine multiple columns in an *or* (select rows that have
data in *any* of a given set of columns), use a matches expression, as
documented below.
If we want to select a column *and* pick only rows that have a value in
this column, a shorthand syntax exists:
vnl-filter --has col -p col
is equivalent to
vnl-filter -p +col
Note that just like the column specifications in "-p" the columns given
to "--has" must match exactly *or* as a regex. In either case, a unique
matching column must be found.
-l|list-columns
Instead of doing any processing, parse the input to get the available
columns, print those out, and exit
-A N|--after-context N
Output N lines following each *matches* expression, even those lines
that do not themselves match. This works just like the "grep" options of
the same name. See "Context lines"
-B N|--before-context N
Output N lines preceding each *matches* expression, even those lines
that do not themselves match. This works just like the "grep" options of
the same name. See "Context lines"
-C N|--context N
Output N lines preceding and following each *matches* expression, even
those lines that do not themselves match. This works just like the
"grep" options of the same name. See "Context lines"
--eval expr
Instead of printing out all matching records and picked columns, just
run the given chunk of awk (or perl). In this mode of operation,
"vnl-filter" acts just like a glorified awk, that allows fields to be
accessed by name instead of by number, as it would be in raw awk.
Since the expression may print *anything* or nothing at all, the output
in this mode is not necessarily itself a valid vnlog stream. And no
column-selecting arguments should be given, since they make no sense in
this mode.
In awk the expr is a full set of pattern/action statements. So to print
the sum of columns "a" and "b" in each row, and at the end, print the
sum of all values in the "a" column
vnl-filter --eval '{print a+b; suma += a} END {print suma}'
In perl the arbitrary expression fits in like this:
sub evalexpr
{
eval expression; # evaluate the arbitrary expression
}
while(<>) # read each line
{
chomp;
next unless matches; # skip non-matching lines
evalexpr();
}
--function|--sub
Evaluates the given expression as a function that can be used in other
expressions. This is most useful when you want to print something that
can't trivially be written as a simple expression. For instance:
$ cat tst.vnl
# s
1-2
3-4
5-6
$ < tst.vnl
vnl-filter --function 'before(x) { sub("-.*","",x); return x }' \
--function 'after(x) { sub(".*-","",x); return x }' \
-p 'b=before(s),a=after(s)'
# b a
1 2
3 4
5 6
See the CAVEATS section below if you're doing something
sufficiently-complicated where you need this.
--function-abs|--sub-abs
Convenience option to add an absolute-value abs() function. This is only
useful for awk programs (the default, no "--perl" given) since perl
already provides abs() by default.
--begin|--BEGIN
Evaluates the given expression in the BEGIN {} block of the generated
awk (or perl) program.
--end|--END
Evaluates the given expression in the END {} block of the generated awk
(or perl) program.
--[no]skipempty
Do [not] skip records where all fields are blank. By default we *do*
skip all empty records; to include them, pass "--noskipempty"
--skipcomments
Don't output non-legend comments
--perl
By default all procesing is performed by "mawk", but if for whatever
reason we want perl instead, pass "--perl". Both modes work, but "mawk"
is noticeably faster. "--perl" could be useful because it is more
powerful, which could be important since a number of things pass
commandline strings directly to the underlying language (named
expressions, matches expressions, "--eval" strings). Note that while
variables in perl use sigils, column references should *not* use sigils.
To print the sum of all values in column "a" you'd do this in awk
vnl-filter --eval '{suma += a} END {print suma}'
and this in perl
vnl-filter --perl --eval '{$suma += a} END {say $suma}'
The perl strings are evaluated without "use strict" or "use warnings" so
I didn't have to declare $suma in the example.
With "--perl", empty strings ("-" in the vnlog file) are converted to
"undef".
--dumpexprs
Used for debugging. This spits out all the final awk (or perl) program
we run for the given commandline options and given input. This is the
final program, with the column references resolved to numeric indices,
so one can figure out what went wrong.
--unbuffered
Flushes each line after each print. This makes sure each line is output
as soon as it is available, which is crucial for realtime output and
streaming plots.
--stream
Synonym for "--unbuffered"
CAVEATS
This tool is very lax in its input validation (on purpose). As a result,
columns with names like %CPU and "TIME+" do work (i.e. you can more or
less feed in output from "top -b"). The downside is that shooting
yourself in the foot is possible. This tradeoff is currently tuned to be
very permissive, which works well for my use cases. I'd be interested in
hearing other people's experiences. Potential pitfalls/unexpected
behaviors:
* All column names are replaced in all eval strings without regard to
context. The earlier example that reports the sum of values in a
column: vnl-filter --eval '{suma += a} END {print suma}' will work
fine if we *do* have a column named "a" and do *not* have a column
named "suma". But will not do the right thing if any of those are
violated. For instance, if a column "a" doesn't exist, then "awk"
would see "suma += a" instead of something like "suma += $5". "a"
would be an uninitialized variable, which evaluates to 0, so the
full "vnl-filter" command would not fail, but would print 0 instead.
It's the user's responsibility to make sure we're talking about the
right columns. The focus here was one-liners so hopefully nobody has
so many columns, they can't keep track of all of them in their head.
I don't see any way to resolve this without seriously impacting the
scope of the tool, so I'm leaving this alone.
* It is natural to use vnlog as a database. You can run queries with
something like
vnl-filter 'key == 5'
This works. But unlike a real database this is clearly a linear
lookup. With large data files, this would be significantly slower
than the logarithmic searches provided by a real database. The
meaning of "large" and "significant" varies, and you should test it.
In my experience vnlog "databases" scale surprisingly well. But at
some point, importing your data to something like sqlite is well
worth it.
* When substituting column names I match *either* a word-nonword
transition ("\b") *or* a whitespace-nonword transition. The word
boundaries is what would be used 99% of the time. But the keys may
have special characters in them, which don't work with "\b". This
means that whitespace becomes important: "1+%CPU" will not be parsed
as expected, which is correct since "+%CPU" is also a valid field
name. But "1+ %CPU" will be parsed correctly, so if you have weird
field names, put the whitespace into your expressions. It'll make
them more readable anyway.
* Strings passed to "-p" are split on "," *except* if the "," is
inside balanced "()". This makes it possible to say things like
vnl-filter --function 'f(a,b) { ... }' -p 'c=f(a,b)'. This is
probably the right behavior, although some questionable looking
field names become potentially impossible: "f(a" and "b)" *could*
otherwise be legal field names, but you're probably asking for
trouble if you do that.
* Currently there're two modes: a pick/print mode and an "--eval"
mode. Then there's also "--function", which adds bits of "--eval" to
the pick/print mode, but it feels maybe insufficient. I don't yet
have strong feelings about what this should become. Comments welcome
NAME
vnl-align - aligns vnlog columns for easy interpretation by humans
SYNOPSIS
$ cat tst.vnl
# w x y z
-10 40 asdf -
-20 50 - 0.300000
-30 10 whoa 0.500000
$ vnl-align tst.vnl
# w x y z
-10 40 asdf -
-20 50 - 0.300000
-30 10 whoa 0.500000
DESCRIPTION
The basic usage is
vnl-align logfile
The arguments are assumed to be the vnlog files. If no arguments are
given, the input comes from STDIN.
This is very similar to "column -t", but handles "#" lines properly:
1. The first "#" line is the legend. For the purposes of alignment, the
leading "#" character and the first column label are treated as one
column
2. All other "#" lines are output verbatim.
NAME
vnl-sort - sorts an vnlog file, preserving the legend
SYNOPSIS
$ cat a.vnl
# a b
AA 11
bb 12
CC 13
dd 14
dd 123
Sort lexically by a:
$ <a.vnl vnl-sort -k a
# a b
AA 11
CC 13
bb 12
dd 123
dd 14
Sort lexically by a, ignoring case:
$ <a.vnl vnl-sort -k a --ignore-case
# a b
AA 11
bb 12
CC 13
dd 123
dd 14
Sort lexically by a, then numerically by b:
$ <a.vnl vnl-sort -k a -k b.n
# a b
AA 11
CC 13
bb 12
dd 14
dd 123
Sort lexically by a, then numerically by b in reverse:
$ <a.vnl vnl-sort -k a -k b.nr
# a b
AA 11
CC 13
bb 12
dd 123
dd 14
Sort by month and then day:
$ cat dat.vnl
# month day
March 5
Jan 2
Feb 1
March 30
Jan 21
$ <dat.vnl vnl-sort -k month.M -k day.n
# month day
Jan 2
Jan 21
Feb 1
March 5
March 30
DESCRIPTION
Usage: vnl-sort [options] logfile logfile logfile ... < logfile
This tool sorts given vnlog files in various ways. "vnl-sort" is a
wrapper around the GNU coreutils "sort" tool. Since this is a wrapper,
most commandline options and behaviors of the "sort" tool are present;
consult the sort(1) manpage for detail. The differences from GNU
coreutils "sort" are
* The input and output to this tool are vnlog files, complete with a
legend
* The columns are referenced by name, not index. So instead of saying
sort -k1
to sort by the first column, you say
sort -k time
to sort by column "time".
* The fancy "KEYDEF" spec from "sort" is only partially supported. I
only allow us to sort by full *fields*, so the start/stop positions
don't make sense. I *do* support the "OPTS" to change the type of
sorting in a given particular column. For instance, to sort by month
and then by day, do this (see example above):
vnl-sort -k month.M -k day.n
* "--files0-from" is not supported due to lack of time. If somebody
really needs it, talk to me.
* "--output" is not supported due to an uninteresting technical
limitation. The output always goes to standard out.
* "--field-separator" is not supported because vnlog assumes
whitespace-separated fields
* "--zero-terminated" is not supported because vnlog assumes
newline-separated records
* By default we call the "sort" tool to do the actual work. If the
underlying tool has a different name or lives in an odd path, this
can be specified by passing "--vnl-tool TOOL"
Past that, everything "sort" does is supported, so see that man page for
detailed documentation. Note that all non-legend comments are stripped
out, since it's not obvious where they should end up.
COMPATIBILITY
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.
SEE ALSO
sort(1)
NAME
vnl-join - joins two log files on a particular field
SYNOPSIS
$ cat a.vnl
# a b
AA 11
bb 12
CC 13
dd 14
dd 123
$ cat b.vnl
# a c
aa 1
cc 3
bb 4
ee 5
- 23
Try to join unsorted data on field 'a':
$ vnl-join -j a a.vnl b.vnl
# a b c
join: /dev/fd/5:3: is not sorted: CC 13
join: /dev/fd/6:3: is not sorted: bb 4
Sort the data, and join on 'a':
$ vnl-join --vnl-sort - -j a a.vnl b.vnl | vnl-align
# a b c
bb 12 4
Sort the data, and join on 'a', ignoring case:
$ vnl-join -i --vnl-sort - -j a a.vnl b.vnl | vnl-align
# a b c
AA 11 1
bb 12 4
CC 13 3
Sort the data, and join on 'a'. Also print the unmatched lines from both files:
$ vnl-join -a1 -a2 --vnl-sort - -j a a.vnl b.vnl | vnl-align
# a b c
- - 23
AA 11 -
CC 13 -
aa - 1
bb 12 4
cc - 3
dd 123 -
dd 14 -
ee - 5
Sort the data, and join on 'a'. Print the unmatched lines from both files,
Output ONLY column 'c' from the 2nd input:
$ vnl-join -a1 -a2 -o 2.c --vnl-sort - -j a a.vnl b.vnl | vnl-align
# c
23
-
-
1
4
3
-
-
5
DESCRIPTION
Usage: vnl-join [join options]
[--vnl-sort -|[sdfgiMhnRrV]+]
[ --vnl-[pre|suf]fix[1|2] xxx |
--vnl-[pre|suf]fix xxx,yyy,zzz |
--vnl-autoprefix |
--vnl-autosuffix ]
logfile1 logfile2
This tool joins two vnlog files on a given field. "vnl-join" is a
wrapper around the GNU coreutils "join" tool. Since this is a wrapper,
most commandline options and behaviors of the "join" tool are present;
consult the join(1) manpage for detail. The differences from GNU
coreutils "join" are
* The input and output to this tool are vnlog files, complete with a
legend
* The columns are referenced by name, not index. So instead of saying
join -j1
to join on the first column, you say
join -j time
to join on column "time".
* -1 and -2 are supported, but *must* refer to the same field. Since
vnlog knows the identify of each field, it makes no sense for -1 and
-2 to be different. So pass "-j" instead, it makes more sense in
this context.
* "-a-" is available as a shorthand for "-a1 -a2": this is a full
outer join, printing unmatched records from both of the inputs.
Similarly, "-v-" is available as a shorthand for "-v1 -v2": this
will output *only* the unique records in both of the inputs.
* "vnl-join"-specific options are available to adjust the field-naming
in the output:
--vnl-prefix1
--vnl-suffix1
--vnl-prefix2
--vnl-suffix2
--vnl-prefix
--vnl-suffix
--vnl-autoprefix
--vnl-autosuffix
See "Field names in the output" below for details.
* A "vnl-join"-specific option "--vnl-sort" is available to sort the
input and/or output. See below for details.
* By default we call the "join" tool to do the actual work. If the
underlying tool has a different name or lives in an odd path, this
can be specified by passing "--vnl-tool TOOL"
* If no "-o" is given, we output the join field, the remaining fields
in logfile1, the remaining fields in logfile2, .... This is what "-o
auto" does, except we also handle empty vnlogs correctly.
* "-e" is not supported because vnlog uses "-" to represent undefined
fields.
* "--header" is not supported because vnlog assumes a specific header
structure, and "vnl-join" makes sure that this header is handled
properly
* "-t" is not supported because vnlog assumes whitespace-separated
fields
* "--zero-terminated" is not supported because vnlog assumes
newline-separated records
* Rather than only 2-way joins, this tool supports N-way joins for any
N > 2. See below for details.
Past that, everything "join" does is supported, so see that man page for
detailed documentation. Note that all non-legend comments are stripped
out, since it's not obvious where they should end up.
Field names in the output
By default, the field names in the output match those in the input. This
is what you want most of the time. It is possible, however that a column
name adjustment is needed. One common use case for this is if the files
being joined have identically-named columns, which would produce
duplicate columns in the output. Example: we fixed a bug in a program,
and want to compare the results before and after the fix. The program
produces an x-y trajectory as a function of time, so both the bugged and
the bug-fixed programs produce a vnlog with a legend
# time x y
Joining this on "time" will produce a vnlog with a legend
# time x y x y
which is confusing, and *not* what you want. Instead, we invoke
"vnl-join" as
vnl-join --vnl-suffix1 _buggy --vnl-suffix2 _fixed -j time buggy.vnl fixed.vnl
And in the output we get a legend
# time x_buggy y_buggy x_fixed y_fixed
Much better.
Note that "vnl-join" provides several ways of specifying this. The above
works *only* for 2-way joins. An alternate syntax is available for N-way
joins, a comma-separated list. The same could be expressed like this:
vnl-join -a- --vnl-suffix _buggy,_fixed -j time buggy.vnl fixed.vnl
Finally, if passing in structured filenames, "vnl-join" can infer the
desired syntax from the filenames. The same as above could be expressed
even simpler:
vnl-join --vnl-autosuffix -j time buggy.vnl fixed.vnl
This works by looking at the set of passed in filenames, and stripping
out the common leading and trailing strings.
Sorting of input and output
The GNU coreutils "join" tool expects sorted columns because it can then
take only a single pass through the data. If the input isn't sorted,
then we can use normal shell substitutions to sort it:
$ vnl-join -j key <(vnl-sort -s -k key a.vnl) <(vnl-sort -s -k key b.vnl)
For convenience "vnl-join" provides a "--vnl-sort" option. This allows
the above to be equivalently expressed as
$ vnl-join -j key --vnl-sort - a.vnl b.vnl
The "-" after the "--vnl-sort" indicates that we want to sort the
*input* only. If we also want to sort the output, pass the short codes
"sort" accepts instead of the "-". For instance, to sort the input for
"join" and to sort the output numerically, in reverse, do this:
$ vnl-join -j key --vnl-sort rg a.vnl b.vnl
The reason this shorthand exists is to work around a quirk of "join".
The sort order is *assumed* by "join" to be lexicographical, without any
way to change this. For "sort", this is the default sort order, but
"sort" has many options to change the sort order, options which are
sorely missing from "join". A real-world example affected by this is the
joining of numerical data. If you have "a.vnl":
# time a
8 a
9 b
10 c
and "b.vnl":
# time b
9 d
10 e
Then you cannot use "vnl-join" directly to join the data on time:
$ vnl-join -j time a.vnl b.vnl
# time a b
join: /dev/fd/4:3: is not sorted: 10 c
join: /dev/fd/5:2: is not sorted: 10 e
9 b d
10 c e
Instead you must re-sort both files lexicographically, *and* then
(because you almost certainly want to) sort it back into numerical
order:
$ vnl-join -j time <(vnl-sort -s -k time a.vnl) <(vnl-sort -s -k time b.vnl) |
vnl-sort -s -n -k time
# time a b
9 b d
10 c e
Yuck. The shorthand described earlier makes the interface part of this
palatable:
$ vnl-join -j time --vnl-sort n a.vnl b.vnl
# time a b
9 b d
10 c e
Note that the input sort is stable: "vnl-join" will invoke "vnl-sort
-s". If you want a stable post-sort, you need to ask for it with
"--vnl-sort s...".
N-way joins
The GNU coreutils "join" tool is inherently designed to join *exactly*
two files. "vnl-join" extends this capability by chaining together a
number of "join" invocations to produce a generic N-way join. This works
exactly how you would expect with the following caveats:
* Full outer joins are supported by passing "-a-", but no other "-a"
option is supported. This is possible, but wasn't obviously worth
the trouble.
* "-v" is not supported. Again, this is possible, but wasn't obviously
worth the trouble.
* Similarly, "-o" is not supported. This is possible, but wasn't
obviously worth the trouble, especially since the desired behavior
can be obtained by post-processing with "vnl-filter".
BUGS AND CAVEATS
The underlying "sort" tool assumes lexicographic ordering, and matches
fields purely based on their textual contents. This means that for the
purposes of joining, 10, 10.0 and 1.0e1 are all considered different. If
needed, you can normalize your keys with something like this:
vnl-filter -p x='sprintf("%f",x)'
COMPATIBILITY
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.
SEE ALSO
join(1)
NAME
vnl-tail - tail a log file, preserving the legend
SYNOPSIS
$ read_temperature | tee temp.vnl
# temperature
29.5
30.4
28.3
22.1
... continually produces data
... at the same time, in another terminal
$ vnl-tail -f temp.vnl
# temperature
28.3
22.1
... outputs data as it comes in
DESCRIPTION
Usage: vnl-tail [options] logfile logfile logfile ... < logfile
This tool runs "tail" on given vnlog files in various ways. "vnl-tail"
is a wrapper around the GNU coreutils "tail" tool. Since this is a
wrapper, most commandline options and behaviors of the "tail" tool are
present; consult the tail(1) manpage for detail. The differences from
GNU coreutils "tail" are
* The input and output to this tool are vnlog files, complete with a
legend
* "-c" is not supported because vnlog really doesn't want to break up
lines
* "--zero-terminated" is not supported because vnlog assumes
newline-separated records
* By default we call the "tail" tool to do the actual work. If the
underlying tool has a different name or lives in an odd path, this
can be specified by passing "--vnl-tool TOOL"
Past that, everything "tail" does is supported, so see that man page for
detailed documentation.
COMPATIBILITY
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.
SEE ALSO
tail(1)
NAME
vnl-ts - add a timestamp to a vnlog stream
SYNOPSIS
$ read_temperature
# temperature
29.5
30.4
28.3
22.1
... continually produces data at 1Hz
$ read_temperature | vnl-ts -s %.s
# time-rel temperature
0.013893 30.2
1.048695 28.6
2.105592 29.3
3.162873 22.0
...
DESCRIPTION
Usage: vnl-ts [-i | -s] [-m] [--vnl-field t] format < pipe
This tool runs "ts" on given vnlog streams. "vnl-ts" is a wrapper around
the "ts" tool from Joey Hess's moreutils
<https://joeyh.name/code/moreutils/> toolkit. Since this is a wrapper,
most commandline options and behaviors of the "ts" tool are present;
consult the ts(1) manpage for details. The differences from "ts" are
* The input and output to this tool are vnlog files, complete with a
legend
* The format *must* be passed-in by the user; no default is assumed.
* The given format *must not* contain whitespace, so that it fits a
single vnlog field.
* "-r" is not supported: it assumes input timestamps with whitespace,
which is incompatible with vnlog
* A "vnl-ts"-specific option "--vnl-field" is available to set the
name of the new field. If omitted, a reasonable default will be
used.
* By default we call the "ts" tool to do the actual work. If the
underlying tool has a different name or lives in an odd path, this
can be specified by passing "--vnl-tool TOOL"
Past that, everything "ts" does is supported, so see that man page for
detailed documentation.
COMPATIBILITY
By default this calls the tool named "ts". At least on FreeBSD, it's
called "moreutils-ts", so on such systems you should invoke "vnl-ts
--vnl-tool moreutils-ts ..."
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.
SEE ALSO
ts(1)
NAME
vnl-uniq - uniq a log file, preserving the legend
SYNOPSIS
$ cat colors.vnl
# color
blue
yellow
yellow
blue
yellow
orange
orange
$ < colors.vnl | vnl-sort | vnl-uniq -c
# count color
2 blue
2 orange
3 yellow
DESCRIPTION
Usage: vnl-uniq [options] < logfile
This tool runs "uniq" on a given vnlog dataset. "vnl-uniq" is a wrapper
around the GNU coreutils "uniq" tool. Since this is a wrapper, most
commandline options and behaviors of the "uniq" tool are present;
consult the uniq(1) manpage for detail. The differences from GNU
coreutils "uniq" are
* The input and output to this tool are vnlog files, complete with a
legend
* "--zero-terminated" is not supported because vnlog assumes
newline-separated records
* Only *one* input is supported (a file on the cmdline or data on
standard input), and the output *always* goes to standard output.
Specifying the output as a file on the commandline is not supported.
* "--vnl-count NAME" can be given to name the "count" column. "-c" is
still supported to add the default new column named "count", but if
another name is wanted, "--vnl-count" does that. "--vnl-count"
implies "-c"
* In addition to the normal behavior of skipping fields at the start,
"-f" and "--skip-fields" can take a negative argument to skip the
*all but the last* N fields. For instance, to use only the one last
field, pass "-f -1" or "--skip-fields=-1".
* By default we call the "uniq" tool to do the actual work. If the
underlying tool has a different name or lives in an odd path, this
can be specified by passing "--vnl-tool TOOL"
Past that, everything "uniq" does is supported, so see that man page for
detailed documentation.
COMPATIBILITY
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.
SEE ALSO
uniq(1)
NAME
vnl-gen-header - create definition for vnlog output from C
SYNOPSIS
$ vnl-gen-header 'int w' 'uint8_t x' 'char* y' 'double z' > vnlog_fields_generated.h
DESCRIPTION
We provide a simple C library to produce vnlog output. The fields this
library outputs must be known at compile time, and are specified in a
header created by this tool. Please see the vnlog documentation for
instructions on how to use the library
ARGUMENTS
This tool needs to be given a list of field definitions. First we look
at the commandline, and if the definitions are not available there, we
look on STDIN. Each definition is a string "type name" (one def per
argument on the commandline or per line on STDIN). If reading from
STDIN, we ignore blank lines, and treat any line starting with "#" as a
comment.
Each def represents a single output field. Each such field spec in a
C-style variable declaration with a type followed by a name. Note that
these field specs contain whitespace, so each one must be quoted before
being passed to the shell.
The types can be basic scalars, possibly with set widths ("char",
"double", "int", "uint32_t", "unsigned int", ...), a NULL-terminated
string ("char*") or a generic chunk of binary data ("void*").
The names must consist entirely of letters, numbers or "_", like
variables in C.
NAME
vnl-make-matrix - create a matrix from a one-point-per-record vnlog
SYNOPSIS
$ cat /tmp/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
$ </tmp/dat.vnl vnl-filter -p i,x | vnl-make-matrix --outdir /tmp --prefix test_
Writing to '/tmp/test_x.matrix'
$ cat /tmp/test_x.matrix
1 2 3
4 5 6
7 8 9
10 11 12
DESCRIPTION
Vnlog represents each "data item" as a line of text. This is very often
what one wants, but at times it isn't. One example of this is matrix
data: we want each line to contain a whole row of a matrix. This script
exists for convenience, to bridge this gap.
The input is an vnlog, coming in on STDIN and/or in files given on the
commandline. This vnlog must have at least two fields: the
least-significant (slowest-changing) index of each point (must be the
*first* field), and as many value fields as desired. These points must
be written out in order, and it is assumed that all entries in the
matrix are specified. The output is a set of (non-vnlog) matrix files in
the directory given in the "--outdir" argument. These files are named
"PREFIX_XXX.matrix" where "PREFIX" comes from --prefix (or empty) and
"XXX" is the field name. These matrices can be loaded into any analysis
tool (numpy for instance), or plotted directly with gnuplot:
set size ratio -1
plot "/tmp/test_x.matrix" matrix with image
pause -1
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.