Command-line tool to build, update and query a persistent set of HEALPix Multi-Order Coverages maps (MOCs)
Project description
moc-set
A command-line tool to build, update and query a persistent set of Multi-Order Coverages maps (MOCs), see this IVOA standard.
About
Query a set of S-MOCs pre-saved in a single large binary file.
The file can be seen as a persistent cache preventing
from having to open/read/parse a possible large set of FITS files.
A moc-set
can be updated by adding or removing MOCs from it, without having
to re-build the full binary file (except from time to time using the purge
command).
It is built in such a way that read operations are allowed while updating (add, remove, change status, purge)
the binary file, but a write operation immediately fails (return status != 0) if another write operation
is already ongoing.
Used by
MOC set in used:
- in production in VizieR when querying a cone
on the
> 16_000
catalogues - in an ongoing project leading by @lmichel to look for XMM FOVs intersecting a user define region.
Similar to the CDS MOC Server.
The CDS MOC Server additionally stores metadata information associated to each MOC, allows queries with constraints on those metadata, and supports T-MOCs and ST-MOCs in addition to S-MOCs.
So, moc-set
offers functionalities similar to a sub-part of the MOC Server functionalities
(except for T-MOCs and ST-MOCs, one could build a MOC Server like service based on moc-set
,
using an additional mechanism to store and filter metadata).
The MOC Server is implemented in Java. All information used by the MOC Server are loaded in memory at service startup. To speed up the starting time, the MOC Server also resort on a binary dump, needing synchronisation mechanisms with the running server data when the list of MOCs is updated.
moc-set
has primarily been developed for VizieR needs: lighter/simpler version of the MOC server, with
less information needed (VizieR already store catalogues metadata), system programming language with no runtime,
possibly less memory available, ...
Install
From pypi for python users
MOCSet is available in pypi,
you can thus install the mocset
executable using pip
:
pip install -U moc-set
mocset --help
Debian package
Download the last mocset_vxx_yyy.deb
corresponding to your architecture
(x86_64_musl
has the most chances to fit your needs)
from the github release page.
Install the .deb
by clicking on it or using the command line:
sudo dpkg -i mocset_vxx_yyy.deb
sudo apt-get install -f
Then you can use the tool:
mocset
man mocset
You can uninstall using, e.g.:
sudo dpkg -r $(dpkg -f mocset_vxx_yyy.deb Package)
Pre-compile binaries for MacOS, Linux and Windows
Download the last mocset-vxx_yyy.tar.gz
corresponding to your architecture
from the github release page.
You probably want ot use:
- Linux:
mocset-vxx-x86_64-unknown-linux-musl.tar.gz
- MacOS:
mocset-vxx-x86_64-apple-darwin.tar.gz
- Windows:
mocset-vxx-.zip
WARNING: for linux, use musl
instead of gnu
(high chances of incompatibility in the latter case)
The tar contains a single executable binary file.
tar xzvf mocset-vxx-yyy.tar.gz
./mocset
Compile from source code
Install rust
(and check that ~/.cargo/bin/
is in your path),
or update the Rust compiler with:
rustup update
Clone the moc lib rust project:
git clone https://github.com/cds-astro/cds-moc-rust
Install from using cargo
:
cargo install --path crates/set
or
RUSTFLAGS='-C target-cpu=native' cargo install --path crates/set
Usage
Exec mocset --help
to get the help message:
> mocset --help
Command-line tool to build, update and query a persistent set of HEALPix Multi-Order Coverages maps (MOCs)
Usage: mocset <COMMAND>
Commands:
make Make a new mocset
append Append the given MOCs to an existing mocset
chgstatus Change the status flag of the given MOCs identifiers (valid, deprecated, removed)
purge Purge the mocset removing physically the MOCs flagged as 'removed'
list Provide the list of the MOCs in the mocset and the associated flags
query Query the mocset
union Union of all MOCs in the moc-set matching a given region
extract Extracts a MOC from the given moc-set
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
MOC set creation
Simply list in a csv file a set of identifier (integer in [0, 281_474_976_710_655]
),
and MOC FITS file path. See e.g the file moclist.txt:
1,data/CDS_B_bax_bax.fits
2,data/CDS_I_172_irs.fits
3,data/CDS_I_274_ccdm.fits
4,data/CDS_I_42_catalog.fits
5,data/CDS_II_203A_faint.fits
6,data/CDS_II_261_GOODS_S.fits
7,data/CDS_II_339_summary.fits
8,data/CDS_II_97_ans.fits
9,data/CDS_III_206_orion.fits
10,data/CDS_III_43_main.fits
...
Then execute moc-set
from the mocset
command:
> mocset make --n128 3 --moc-list moclist.txt --delimiter , mocset.bin
or from the source code, installing the Rust compiler (including Cargo):
> cargo run --release -- make --n128 3 --moc-list moclist.txt --delimiter , mocset.bin
To build the moc-set binary file mocset.bin
.
The total number of MOCs that can be stored in the file equals `n128 * 128 - 1 (so 383 in the example above, since n128=3).
See the help message for more details:
> mocset make --help
Make a new mocset
Usage: mocset make [OPTIONS] <FILE>
Arguments:
<FILE> Output file, storing the MOC set
Options:
-l, --moc-list <FILE> Input file containing the 'moc_id moc_path' list (default: read from stdin) 'moc_id' must be a positive integer smaller than 281_474_976_710_655 (can be stored on 6 bytes). Use a negative value to flag as deprecated
-d, --delimiter <SEPARATOR> Delimiter used to separate the moc identifier from the moc path [default: " "]
-n, --n128 <N128> n x 128 - 1 = number of MOCs that can be stored in this moc set [default: 1]
-h, --help Print help
List the content of a MOC set
Simply use mocset list
:
> mocset list mocset.bin
id,status,depth,n_ranges,byte_size
1,valid,11,1673,13384
2,valid,11,36022,288176
3,valid,11,55470,443760
4,valid,11,587,4696
5,valid,11,534,4272
6,valid,11,17,136
...
status
: can bevalid
,deprecated
orremoved
n_ranges
: number of ranges in the MOCbyte_size
: size of the MOC stored in the MOC set (in bytes)
See the help message:
> mocset list --help
Provide the list of the MOCs in the mocset and the associated flags
Usage: mocset list [OPTIONS] <FILE>
Arguments:
<FILE> The moc-set to be read
Options:
-r, --ranges Print byte ranges instead of byte_size
-h, --help Print help
Querying a MOC set
See the help to get the different query modes:
> mocset query --help
Query the mocset
Usage: mocset query [OPTIONS] <FILE> <COMMAND>
Commands:
pos Single position
cone A cone, i.e. a position with a small area around (approximated by a MOC)
moc The given MOC (you create a moc using moc-cli and pipe it into moc-set)
help Print this message or the help of the given subcommand(s)
Arguments:
<FILE> The moc-set to be read
Options:
-d, --add-deprecated Also selects MOCs flagged as deprecated
-c, --print-coverage Print in output the sky fraction (in '[0.0, 1.0]') covered by each selected MOC
-p, --parallel <PARALLEL> Switch on multi-threading, with 'parallel' threads (made for SSD, not HDD)
-h, --help Print help
Query for a single position
To obtain the list of the MOCs containing a the position 90.0 +0.0 (in decimal degrees), use:
> mocset query moclist.bin pos 90.0 +0.0
id
161
The result is the list of the identifier of the MOC covering the input position (only one MOC, with identifier 161 in our example).
See the full help:
> mocset query pos --help
Single position
Usage: mocset query <FILE> pos <LON_DEG> <LAT_DEG>
Arguments:
<LON_DEG> Longitude of the cone center (in degrees)
<LAT_DEG> Latitude of the cone center (in degrees)
Options:
-h, --help Print help
Query for a cone
To obtain the list of the MOCs overlapping the cone of center 90.0 +0.0 and having a radius of 320 arcsec, use:
> mocset query mocset.bin cone 90.0 +0.0 320.0 --precision 5
id
2
3
35
161
--precision
is optional, its default value is 2:
- at a
precision
of 0,mocset
transforms the input cone in a MOC containing 1 to 9 values. - at a
precision
of 1,mocset
transforms the input cone in a MOC containing 1 to9x4
values. - at a
precision
ofn
,mocset
transforms the input cone in a MOC containing 1 to9x4^n
values.
See the help:
> mocset query cone --help
A cone, i.e. a position with a small area around (approximated by a MOC)
Usage: mocset query <FILE> cone [OPTIONS] <LON_DEG> <LAT_DEG> <R_ARCSEC>
Arguments:
<LON_DEG> Longitude of the cone center (in degrees)
<LAT_DEG> Latitude of the cone center (in degrees)
<R_ARCSEC> Radius of the cone (in arcseconds)
Options:
-p, --precision <PREC> MOC precision; 0: depth 'd' at which the cone is overlapped by 1 to max 9 cells; 1: depth 'd' + 1; n: depth 'd' + n [default: 2]
-i, --included Returns MOCs containing the whole cone MOC (instead of overlapping only)
-h, --help Print help
Query for a MOC
To obtain the list of the MOCs overlapping the MOC stored in a given FITs file, e.g the MOC of XMM4 DR9, use:
> mocset query mocset.bin moc YOUR_PATH/CDS_IX_59_xmm4dr9s.fits
id
1
2
3
4
5
6
7
8
9
10
...
You may also use a MOC generate on the fly using moc-cli
> moc from polygon 5 "(0.0,0.0),(10.0,0.0),(0.0,10.0)" ascii | mocset query mocset.bin moc - --format ascii
id
1
2
3
4
7
8
13
26
27
35
36
60
63
...
See the help
> mocset query moc --help
The given MOC (you create a moc using moc-cli and pipe it into moc-set)
Usage: mocset query <FILE> moc [OPTIONS] <FILE>
Arguments:
<FILE> Path of the input MOC file (or stdin if equals "-")
Options:
-f, --format <INPUT_FMT> Format of the input MOC ('ascii', 'json' or 'fits') [default: guess from the file extension]
-i, --included Returns MOCs containing the whole given MOC (instead of overlapping)
-h, --help Print help
Query from a STC-S region
You can query from a STC-S region using moc-cli
:
echo "Intersection ICRS (
Polygon 272.536719 -19.461249 272.542612 -19.476380 272.537389 -19.491509 272.540192 -19.499823
272.535455 -19.505218 272.528024 -19.505216 272.523437 -19.500298 272.514082 -19.503376
272.502271 -19.500966 272.488647 -19.490390 272.481932 -19.490913 272.476737 -19.486589
272.487633 -19.455645 272.500386 -19.444996 272.503003 -19.437557 272.512303 -19.432436
272.514132 -19.423973 272.522103 -19.421523 272.524511 -19.413250 272.541021 -19.400024
272.566264 -19.397500 272.564202 -19.389111 272.569055 -19.383210 272.588186 -19.386539
272.593376 -19.381832 272.596327 -19.370541 272.624911 -19.358915 272.629256 -19.347842
272.642277 -19.341020 272.651322 -19.330424 272.653174 -19.325079 272.648903 -19.313708
272.639616 -19.311098 272.638128 -19.303083 272.632705 -19.299839 272.627971 -19.289408
272.628226 -19.276293 272.633750 -19.270590 272.615109 -19.241810 272.614704 -19.221196
272.618224 -19.215572 272.630809 -19.209945 272.633540 -19.198681 272.640711 -19.195292
272.643028 -19.186751 272.651477 -19.182729 272.649821 -19.174859 272.656782 -19.169272
272.658933 -19.161883 272.678012 -19.159481 272.689173 -19.176982 272.689395 -19.183512
272.678006 -19.204016 272.671112 -19.206598 272.664854 -19.203523 272.662760 -19.211156
272.654435 -19.214434 272.652969 -19.222085 272.656724 -19.242136 272.650071 -19.265092
272.652868 -19.274296 272.660871 -19.249462 272.670041 -19.247807 272.675533 -19.254935
272.673291 -19.273917 272.668710 -19.279245 272.671460 -19.287043 272.667507 -19.293933
272.669261 -19.300601 272.663969 -19.307130 272.672626 -19.308954 272.675225 -19.316490
272.657188 -19.349105 272.657638 -19.367455 272.662447 -19.372035 272.662232 -19.378566
272.652479 -19.386871 272.645819 -19.387933 272.642279 -19.398277 272.629282 -19.402739
272.621487 -19.398197 272.611782 -19.405716 272.603367 -19.404667 272.586162 -19.422703
272.561792 -19.420008 272.555815 -19.413012 272.546500 -19.415611 272.537427 -19.424213
272.533081 -19.441402
Not (Polygon 272.511081 -19.487278 272.515300 -19.486595 272.517029 -19.471442
272.511714 -19.458837 272.506430 -19.459001 272.496401 -19.474322 272.504821 -19.484924)
Not (Polygon 272.630446 -19.234210 272.637274 -19.248542 272.638942 -19.231476 272.630868 -19.226364)
)" | moc from stcs 14 - ascii | mocset query mocset.bin moc - --format ascii
Generic parameter
For all queries, the option --add-deprecated
(or -d
) add the MOCs flagged as deprecated in
the output, e.g.:
mocset query --add-deprecated moclist.bin pos 90.0 +0.0 --precision 5
Updating a MOC set
You can:
chgstatus
change the status of a MOC in the MOC set to flag it asdeprecated
or back tovalid
, or asremoved
(WARNING: once removed, a MOC cannot be flagged back asdeprecated
orvalid
)append
a new MOC at the end of the MOC set, the ID of a removed MOC can be reusedpurge
a MOC set to physically remove all MOCs flagged asremoved
. This process basically re-write the whole MOC set file.
Example of usage of chgstatus
> mocset list mocset.bin
id,status,depth,n_ranges,byte_size
1,valid,11,1673,13384
2,valid,11,36022,288176
...
> mocset chgstatus mocset.bin 1 deprecated
> mocset list mocset.bin
id,status,depth,n_ranges,byte_size
1,deprecated,11,1673,13384
2,valid,11,36022,288176
...
> mocset chgstatus mocset.bin 1 valid
> mocset list mocset.bin
id,status,depth,n_ranges,byte_size
1,valid,11,1673,13384
2,valid,11,36022,288176
...
> mocset chgstatus mocset.bin 1 removed
> mocset list mocset.bin
id,status,depth,n_ranges,byte_size
1,removed,11,1673,13384
2,valid,11,36022,288176
...
Example of usage of append
:
> mocset append mocset.bin 3000 MY_PATH/my_new_moc.fits
Example of usage of purge
:
> mocset purge mocset.bin
Help messages:
> mocset chgstatus --help
Change the status flag of the given MOCs identifiers (valid, deprecated, removed)
Usage: mocset chgstatus <FILE> <NEW_STATUS> [IDS]...
Arguments:
<FILE> The moc-set to be updated
<NEW_STATUS> New status flag to be set
[IDS]... Comma separated list of identifiers of the MOCs we want to modify the flag
Options:
-h, --help Print help
> mocset append --help
Append the given MOCs to an existing mocset
Usage: mocset append <FILE> <ID> <MOC_PATH>
Arguments:
<FILE> The moc-set to be updated
<ID> Identifier of the MOC we want to append. 'moc_id' must be a positive integer smaller than 281_474_976_710_655 (can be stored on 6 bytes). Use a negative value to flag as deprecated
<MOC_PATH> Path of the MOC to be append
Options:
-h, --help Print help
> mocset purge --help
Purge the mocset removing physically the MOCs flagged as 'removed'
Usage: mocset purge [OPTIONS] <FILE>
Arguments:
<FILE> The moc-set file to be purge
Options:
-n, --n128 <N128> n x 128 - 1 = number of MOCs that can be stored in this purged moc set, if larger than the current value
-h, --help Print help
Implementation information
Principle
We resort on mapped files and the system disk cache.
Although the first moc-set
query may still be quite long,
the performances of subsequent queries will depend on the ability
of the system to keep the file's data in the disk cache.
Remark
If used on a server with a lot of I/O, the data may not stay in the disk cache for long. If we nevertheless want to always answer quickly, there is at least three options:
- write a daemon loading the full dataset in memory
- create a VM (or a docker?) containing only the
moc-set
tool - my favourite one: use shared memory, resorting e.g. on the shared_memory crate
File structure
The structure of the file is made of two main blocks:
- a fixed length header, made of
- a fixed length metadata
- a fixed length cumulative byte index
- a extensible data part
Metadata part
A fixed size (chosen at creation) buffer of n
u64
elements.
- the first
u64
contains an indication on the buffer size - all other
u64
values, one per MOC in themoc-set
, are made of 3 components:- a
u8
flag taking 4 possible values (only 2 bits are used, 6 are remaining):Valid
MOCDeprecated
MOCRemoved
MOCFree
slot
- the depth of the MOC, stored on `u8 (max depth = 64, thus 2 bits are remaining and could be used)
- the MOC identifier, stored on the 6 remaining bytes.
- a
We stop reading the metadata when we encounter the first Free
flag.
The file can store n - 1
MOCs.
Cumulative byte index
A fixed size (chosen at creation) buffer of n
u64
elements.
- the first
u64
contains the byte size of the header, i.e. the size of the file with no data it also correspond to the starting byte of the first MOC that will be inserted in themoc-set
; - all other elements at index
i
contains the size of the file if only storing the $i+1$ first MOCs.
To get the size (in bytes) of the MOC at index i
, we can simply perform the operation:
cumulIndex[i + 1] - cumulIndex[i]
.
Data part
A simple concatenation of the MOCs ranges.
According to the depth of each MOC, the ranges are either ranges of u32
or ranges of u64
.
Updates and Reading while writing
The only MOC information that can be modified (re-written) is its status flag.
But the status flag is coded on a single byte and a CPU read and write single bytes atomically.
Although, several cores may see the byte in a different state, it is not critical:
a MOC flagged as 'deprecated' or 'deleted' is still physically stored in the moc-set
,
and we can accept a small delay in changing its state.
- Read operation order
- do not need a read lock
- read the metadata part of the header
- read the cumulative bytes index in the header
- read the MOC(s)
- Write Operation order
- ask for a write lock (create a .lock file)
- append the new MOC(s) to the end of the file
- append the new entries to the cumulative bytes index
- possibly update the flag of existing MOCs and append new entries to the end of the header
The header, i.e. both the metadata and the cumulative byte index, is of fixed size,
with free space reserved at file creation.
If a problem occurs while writing, the update is simply going to be ignored
(except the part written in the meta): at the next write operation, if the meta
has not been written (and it is the last part to be written), the code assumes
that the cumulative index beyond the know meta elements is free, the same for the
data byte beyond the last known cumulative index byte.
If a process is reading while another is writing, the newly written part will also simply be ignored if the metadata part has not yet been updated/written.
It works well because we only append new MOCs (we never delete information), we only update metadata to flag a MOC as removed of deprecated, and we respect the read/write order as described above.
Mocset file before adding a new MOC
Add a new moc step 1/3
add a new moc step 2/3
add a new moc step 3/3
Mocset file after having added a new MOC
Purge
The purge operation is the only one removing physically stored MOCs.
It actually consists in building a new moc-set
, removing the MOCs flagged as removed,
in a temporary file, and then making a move replacing the previous moc-set
by the new one.
The purge
operation uses a write lock.
Recall
- Drop linux disk cache, in root mode:
sync; echo 3 > /proc/sys/vm/drop_caches
- Build for being compatible with a large range of systems, avoiding the GLIBC version error (see this post):
cargo build --target x86_64-unknown-linux-musl
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