Data acquisition functions

These functions are used internally and none are exported.

These functions depend on the particulars of the simulation code (e.g. units).

These function read the different output files from the simulation (snapshots, FoF catalogs, sfr.txt, etc.), and load the data into memory as dictionaries.

GalaxyInspector.addRequest — Method

addRequest(
    request::Dict{Symbol,Vector{String}},
    addition::Dict{Symbol,Vector{String}},
)::Dict{Symbol,Vector{String}}

Add the blocks in addition to request, only for the types already present in request.

Arguments

request::Dict{Symbol,Vector{String}}: The request dictionary for readSnapshot.
addition::Dict{Symbol,Vector{String}}: Request dictionary with the blocks to be added, only for the types already present in request.

Returns

A new dictionary with all the requests.

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GalaxyInspector.countSnapshot — Method

countSnapshot(simulation_path::String)::Int

Count the number of snapshots in simulation_path.

Note

This function count the number of snapshots, no the number of snapshot files. So if each snapshot is made of more than one files, the count will not change.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.

Returns

The number of snapshots.

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GalaxyInspector.countStars — Method

countStars(path::String)::Int

Count the number of stars in a snapshot, excluding wind particles.

Arguments

path::String: Path to the snapshot file or folder.

Returns

The number of stars.

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GalaxyInspector.findQtyExtrema — Method

findQtyExtrema(
    simulation_path::String,
    slice_n::Int,
    component::Symbol,
    block::String;
    <keyword arguments>
)::NTuple{2,<:Number}

Compute the minimum and maximum values of block.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.
slice_n::Int: Selects which snapshot to plot, starts at 1 and is independent of the number in the file name. If every snapshot is present, the relation is slice_n = (number in filename) + 1. If set to a negative number, the values in the whole simulation will be compared.
component::Symbol: Cell/particle type. The possibilities are the keys of PARTICLE_INDEX.
block::String: Target block. The possibilities are the keys of QUANTITIES.
f::Function=identity: A function with the signature:
f(data) -> values
where
- data::VecOrMat{<:Number}: Data returned by getBlock.
- values::Vector{<:Number}: A vector with the values to be compared.

Returns

Tuple with the minimum and maximum values.

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GalaxyInspector.findRealStars — Method

findRealStars(path::String)::Vector{Bool}

Find which stellar particles are real stars and not wind particles.

Arguments

path::String: Path to the snapshot file or folder.

Returns

A boolean vector with true for stars and false for wind particles.

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GalaxyInspector.getBlock — Method

getBlock(path::String, component::Symbol, block::String)::VecOrMat{<:Number}

Convenience function to directly get the data associated with one block.

Arguments

path::String: Path to the snapshot file or folder.
component::Symbol: Type of cell/particle. The possibilities are the keys of PARTICLE_INDEX.
block::String: Target block. The possibilities are the keys of QUANTITIES.

Returns

The data for block.

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GalaxyInspector.getGroupCatPaths — Method

getGroupCatPaths(simulation_path::String)::Dict{Symbol,Vector{String}}

Find the path and number of every group catalog in simulation_path.

Note

If each group catalog is made of multiple files, the :paths field will have paths to folders, each one containing the sub-files of the corresponding group catalog.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.

Returns

A dictionary with the following shape:
- :numbers -> The number that characterize each group catalog.
- :paths -> The full path to each group catalog.

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GalaxyInspector.getSnapshotPaths — Method

getSnapshotPaths(simulation_path::String)::Dict{Symbol,Vector{String}}

Find the path and number of every snapshot in simulation_path.

Note

If each snapshot is made of multiple files, the :paths field will have paths to folders, each one containing the sub-files of the corresponding snapshot.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.

Returns

A dictionary with the following shape:
- :numbers -> The number that characterize each snapshot.
- :paths -> The full path to each snapshot.

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GalaxyInspector.groupcatTypes — Method

groupcatTypes(data_dict::Dict)::Vector{Symbol}

Find which group catalog data types are part of the keys of data_dict.

Arguments

data_dict::Dict: A dictionary.

Returns

A vector with the group catalog data types.

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GalaxyInspector.groupcatTypes — Method

groupcatTypes(path::String)::Vector{Symbol}

Find which group catalog data types are part of the snapshot in path.

Note

If each snapshot is made of multiple files, the function will check the first chunk.

Arguments

path::String: Path to the snapshot file or folder.

Returns

A vector with the group catalog data types.

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GalaxyInspector.internalUnits — Method

internalUnits(quantity::String, path::String)::Union{Unitful.Quantity,Unitful.Units}

Get the factor to convert a plain number into a Unitful quantity, using the correct internal code units.

Arguments

quantity::String: Target quantity. The options are the keys of QUANTITIES.
path::String: Path to the snapshot file or folder.

Returns

A Unitful quantity or unit.

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GalaxyInspector.isBlockPresent — Method

isBlockPresent(block::String, group::HDF5.Group)::Bool

Checks if a given data block exists in a HDF5 group.

Arguments

block::String: Target block. The possibilities are the keys of QUANTITIES.
group::HDF5.Group: HDF5 group.

Returns

If block exists in group.

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GalaxyInspector.isBlockPresent — Method

isBlockPresent(component::Symbol, block::String, path::String)::Bool

Checks if a given block exists in a snapshot.

Note

If each snapshot is made of multiple files, the function will only check the first chunk.

Arguments

component::Symbol: The cell/particle type of the target block. The possibilities are the keys of PARTICLE_INDEX.
block::String: Target block. The possibilities are the keys of QUANTITIES.
path::String: Path to the snapshot file or folder.

Returns

If block exists in the snapshot.

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GalaxyInspector.isCosmological — Method

isCosmological(path::String)::Bool

Check if the snapshot in path comes from a cosmological simulation.

Note

If each snapshot is made of multiple files, the function will read the first chunk to check if the simulation is cosmological.

Arguments

path::String: Path to the snapshot file or folder.

Returns

If the simulation is cosmological
- false -> Newtonian simulation (ComovingIntegrationOn = 0, Redshift = 0.0).
- true -> Cosmological simulation (ComovingIntegrationOn = 1, Redshift != 0.0).

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GalaxyInspector.isSubfindActive — Method

isSubfindActive(path::String)::Bool

Check if there is information about the halos and subhalos in the group catalog file.

Arguments

path::String: Path to the group catalog file or folder.

Returns

If there are halo and subhalo information in the group catalog file.

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GalaxyInspector.makeDataDict — Method

makeDataDict(
    simulation_path::String,
    slice_n::Int,
    request::Dict{Symbol,Vector{String}},
    simulation_table::DataFrame,
)::Dict

Construct a data dictionary for a single snapshot.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.
slice_n::Int: Selects the target snapshot. Starts at 1 and is independent of the number in the file name. If every snapshot is present, the relation is slice_n = (number in filename) + 1.
request::Dict{Symbol,Vector{String}}: Dictionary with the shape cell/particle type -> [block, block, ...], where the possible types are the keys of PARTICLE_INDEX, and the possible quantities are the keys of QUANTITIES.
simulation_table::DataFrame: Dataframe with the path, time stamps, and number of each snapshot and group catalog file in simulation_path. It must have the same shape as the one returned by makeSimulationTable.

Returns

A dictionary with the following shape:
- :sim_data -> ::Simulation (see Simulation).
- :snap_data -> ::Snapshot (see Snapshot).
- :gc_data -> ::GroupCatalog (see GroupCatalog).
- cell/particle type -> (block -> data of block, block -> data of block, ...).
- cell/particle type -> (block -> data of block, block -> data of block, ...).
- cell/particle type -> (block -> data of block, block -> data of block, ...).
- ...
- groupcat type -> (block -> data of block, block -> data of block, ...).
- groupcat type -> (block -> data of block, block -> data of block, ...).
- groupcat type -> (block -> data of block, block -> data of block, ...).
- ...

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GalaxyInspector.makeDataDict — Method

makeDataDict(
    simulation_path::String,
    slice_n::Int,
    request::Dict{Symbol,Vector{String}},
)::Dict

Construct a data dictionary for a single snapshot.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.
slice_n::Int: Selects the target snapshot. Starts at 1 and is independent of the number in the file name. If every snapshot is present, the relation is slice_n = (number in filename) + 1.
request::Dict{Symbol,Vector{String}}: Dictionary with the shape cell/particle type -> [block, block, ...], where the possible types are the keys of PARTICLE_INDEX, and the possible quantities are the keys of QUANTITIES.

Returns

A dictionary with the following shape:
- :sim_data -> ::Simulation (see Simulation).
- :snap_data -> ::Snapshot (see Snapshot).
- :gc_data -> ::GroupCatalog (see GroupCatalog).
- cell/particle type -> (block -> data of block, block -> data of block, ...).
- cell/particle type -> (block -> data of block, block -> data of block, ...).
- cell/particle type -> (block -> data of block, block -> data of block, ...).
- ...
- groupcat type -> (block -> data of block, block -> data of block, ...).
- groupcat type -> (block -> data of block, block -> data of block, ...).
- groupcat type -> (block -> data of block, block -> data of block, ...).
- ...

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GalaxyInspector.makeSimulationTable — Method

makeSimulationTable(simulation_path::String)::DataFrame

Construct a dataframe with the path, time stamps and number of each snapshot and group catalog file in simulation_path.

Arguments

simulation_path::String: Path to the simulation directory, set in the code variable OutputDir.

Returns

A dataframe with 8 columns:
- :ids -> Dataframe index of each snapshot, i.e. if there are 10 snapshots in total it runs from 1 to 10.
- :numbers -> Number in the file name of each snapshot.
- :scale_factors -> Scale factor of each snapshot.
- :redshifts -> Redshift of each snapshot.
- :physical_times -> Physical time since the Big Bang of each snapshot.
- :lookback_times -> Physical time left to reach the last snapshot.
- :snapshot_paths -> Full path to the snapshots.
- :groupcat_paths -> Full path to the group catalog files.

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GalaxyInspector.mergeRequests — Method

mergeRequests(requests::Dict{Symbol,Vector{String}}...)::Dict{Symbol,Vector{String}}

Merge several request dictionaries, ignoring duplicates.

Arguments

requests: The request dictionaries for readSnapshot.

Returns

A new dictionary with all the requests.

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GalaxyInspector.readCpuFile — Method

readCpuFile(
    file_path::String,
    targets::Vector{String};
    <keyword arguments>
)::Dict{String,Matrix{Float64}}

Read the cpu.txt file.

For each process in targets a matrix with all the CPU usage data is returned.

Arguments

file_path::String: Path to the cpu.txt file.
targets::Vector{String}: Target processes.
step::Int=1: Step used to traverse the rows.

Returns

A dictionary with the following shape:
target process -> matrix with columns:
- Time step.
- Simulation time (scale factor for cosmological simulations and physical time for non-cosmological simulations).
- Clock time in seconds.
- Clock time as a percentage.
- Total clock time in seconds.
- Total clock time as a percentage.

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GalaxyInspector.readGoupCatBlocks — Method

readGoupCatBlocks(
    file_path::String,
    snapshot_path::String,
    request::Dict{Symbol,Vector{String}},
)::Dict{Symbol,Dict{String,VecOrMat{<:Number}}}

Read the specified blocks from a group catalog file.

Arguments

file_path::String: Path to the group catalog file.
snapshot_path::String: Path to the corresponding snapshot file or folder. This is needed for unit conversion.
request::Dict{Symbol,Vector{String}}: The blocks to be read. It must have the shape group type -> [block, block, block].

Returns

A dictionary with the following shape: group type -> (block -> data of block).

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GalaxyInspector.readGroupCatHeader — Method

readGroupCatHeader(path::Union{String,Missing})::GroupCatHeader

Read the header of a group catalog in the HDF5 format.

Note

If each group catalog is made of multiple files, the function will read the header of the first one.

Arguments

path::Union{String,Missing}: Path to the group catalog file or folder.

Returns

A GroupCatHeader.

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GalaxyInspector.readGroupCatalog — Method

readGroupCatalog(
    path::Union{String,Missing},
    snapshot_path::String,
    request::Dict{Symbol,Vector{String}},
)::Dict{Symbol,Dict{String,VecOrMat{<:Number}}}

Read the specified blocks from a group catalog file or folder.

Arguments

path::Union{String,Missing}: Path to the group catalog file or folder.
snapshot_path::String: Path to the corresponding snapshot file or folder. This is needed for unit conversion.
request::Dict{Symbol,Vector{String}}: Which blocks will be read. It must have the shape group type -> [block, block, block].

Returns

A dictionary with the following shape: group type -> (block -> data of block).

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GalaxyInspector.readSfrFile — Method

readSfrFile(
    file_path::String,
    snap_path::String,
)::Dict{Int32,VecOrMat{<:Number}}

Read the sfr.txt file.

Arguments

file_path::String: Path to the sfr.txt file.
snapshot_path::String: Path to one snapshot file or folder of the simulation. This is needed for unit conversion.

Returns

A dictionary with the following shape:
- 1 -> Time or scale factor (internal units).
- 2 -> Total stellar mass to be formed prior to stochastic sampling (internal units).
- 3 -> Instantaneous star formation rate of all cells ($\mathrm{M_\odot \, yr^{-1}}$).
- 4 -> Instantaneous star formation rate of active cells ($\mathrm{M_\odot \, yr^{-1}}$).
- 5 -> Total mass in stars formed after stochastic sampling (internal units).
- 6 -> Cumulative stellar mass formed (internal units).

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GalaxyInspector.readSnapBlocks — Method

readSnapBlocks(
    file_path::String,
    request::Dict{Symbol,Vector{String}},
)::Dict{Symbol,Dict{String,VecOrMat{<:Number}}}

Read the specified blocks from a snapshot file.

Arguments

file_path::String: Path to the snapshot file.
request::Dict{Symbol,Vector{String}}: The blocks to be read. It must have the shape cell/particle type -> [block, block, block].

Returns

A dictionary with the following shape: cell/particle type -> (block -> data of block).

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GalaxyInspector.readSnapHeader — Method

readSnapHeader(path::String)::SnapshotHeader

Read the header of a snapshot in the HDF5 format.

Note

If each snapshot is made of multiple files, the function will read the header of the first chunk.

Arguments

path::String: Path to the snapshot file or folder.

Returns

A SnapshotHeader structure.

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GalaxyInspector.readSnapshot — Method

readSnapshot(
    path::Union{String,Missing},
    request::Dict{Symbol,Vector{String}},
)::Dict{Symbol,Dict{String,VecOrMat{<:Number}}}

Read the specified blocks from a snapshot file or folder.

Arguments

path::Union{String,Missing}: Path to the snapshot file or folder.
request::Dict{Symbol,Vector{String}}: Which blocks will be read. It must have the shape cell/particle type -> [block, block, block].

Returns

A dictionary with the following shape: cell/particle type -> (block -> data of block).

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GalaxyInspector.readTemperature — Method

readTemperature(file_path::String)::Vector{<:Unitful.Temperature}

Compute the temperature of the gas cells in a snapshot.

Arguments

file_path::String: Path to the snapshot file.

Returns

The temperature of the gas cells.

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GalaxyInspector.readTime — Method

readTime(path::String)::Float64

Read the "Time" field in the header of a snapshot file.

Note

If each snapshot is made of multiple files, the function will read the header of the first chunk.

Arguments

path::String: Path to the snapshot file or folder.

Returns

The "Time" field in the header (for cosmological simulations it is the scale factor).

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GalaxyInspector.snapshotTypes — Method

snapshotTypes(data_dict::Dict)::Vector{Symbol}

Find which cell/particle types are part of the keys of data_dict.

Arguments

data_dict::Dict: A dictionary.

Returns

A vector with the cell/particle types.

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GalaxyInspector.snapshotTypes — Method

snapshotTypes(path::String)::Vector{Symbol}

Find which cell/particle types are part of the snapshot in path.

Note

If each snapshot is made of multiple files, the function will check the first chunk.

Arguments

path::String: Path to the snapshot file or folder.

Returns

A vector with the cell/particle types.

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