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Merge pull request #22 from psrenergy/vj/update-reader
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update reader and csv goto
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@guilhermebodin
guilhermebodin authored Sep 16, 2024
2 parents 7d144df + cb10f65 commit f9112c2
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Showing 4 changed files with 180 additions and 38 deletions.
8 changes: 5 additions & 3 deletions src/binary.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -107,14 +107,16 @@ function Reader{binary}(

io = open(filename_with_extensions, "r")

last_dimension_read = zeros(Int, metadata.number_of_dimensions)
dimension_in_cache = zeros(Int, metadata.number_of_dimensions)
dimension_to_read = zeros(Int, metadata.number_of_dimensions)

reader = try
Quiver.Reader{binary}(
io,
filename,
metadata,
last_dimension_read;
dimension_in_cache,
dimension_to_read;
labels_to_read = isempty(labels_to_read) ? metadata.labels : labels_to_read,
carrousel = carrousel,
)
Expand All @@ -127,7 +129,7 @@ function Reader{binary}(
end

function _quiver_goto!(reader::Quiver.Reader{binary})
next_pos = _calculate_position_in_file(reader.metadata, reader.last_dimension_read...)
next_pos = _calculate_position_in_file(reader.metadata, reader.dimension_to_read...)
# Check if we need to seek a new position or write directly in the io
# This is absolutely necessary for performance in the binary operation
current_pos = position(reader.reader)
Expand Down
57 changes: 31 additions & 26 deletions src/csv.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,8 @@ function Reader{csv}(
reusebuffer = true,
)

last_dimension_read = zeros(Int, metadata.number_of_dimensions)
dimension_in_cache = zeros(Int, metadata.number_of_dimensions)
dimension_to_read = zeros(Int, metadata.number_of_dimensions)

next = iterate(rows)
(row, state) = next
Expand All @@ -92,7 +93,8 @@ function Reader{csv}(
row_reader,
filename,
metadata,
last_dimension_read;
dimension_in_cache,
dimension_to_read;
labels_to_read = isempty(labels_to_read) ? metadata.labels : labels_to_read,
carrousel = carrousel,
)
Expand All @@ -111,7 +113,7 @@ function _quiver_next_dimension!(reader::Quiver.Reader{csv})
end
(row, state) = reader.reader.next
for (i, dim) in enumerate(reader.metadata.dimensions)
reader.last_dimension_read[i] = row[dim]
reader.dimension_to_read[i] = row[dim]
end
for (i, ts) in enumerate(reader.metadata.labels)
reader.all_labels_data_cache[i] = row[Symbol(ts)]
Expand Down Expand Up @@ -151,38 +153,41 @@ function _quiver_goto!(reader::Quiver.Reader{csv})
return nothing
end

dimension_in_cache = reader.dimension_in_cache
dimension_to_read = reader.dimension_to_read
dimension_in_iterator = _current_dimension_in_iterator(reader)
dimension_to_read = reader.last_dimension_read

order_of_dimension_in_iterator = _calculate_order_in_file(reader.metadata, dimension_in_iterator...)
order_of_dimension_to_read = _calculate_order_in_file(reader.metadata, dimension_to_read...)

if order_of_dimension_in_iterator > order_of_dimension_to_read
error("Cannot read a dimension that is posterior to the current dimension")
elseif order_of_dimension_in_iterator == order_of_dimension_to_read
if dimension_to_read == reader.metadata.dimension_size
(row, state) = reader.reader.next
is_first_index = true
for (i, dim) in enumerate(reader.metadata.dimensions)
reader.last_dimension_read[i] = row[dim]
is_first_index = is_first_index && row[dim] == 1
reader.dimension_to_read[i] = row[dim]
end

for (i, ts) in enumerate(reader.metadata.labels)
if is_first_index
reader.all_labels_data_cache[i] = row[Symbol(ts)]
else
reader.all_labels_data_cache[i] = row[Symbol(ts)]
end
return nothing
end

order_of_dimension_in_cache = _calculate_order_in_file(reader.metadata, dimension_in_cache...)
order_of_dimension_to_read = _calculate_order_in_file(reader.metadata, dimension_to_read...)
order_of_dimension_in_iterator = _calculate_order_in_file(reader.metadata, dimension_in_iterator...)

if order_of_dimension_in_cache > order_of_dimension_to_read
error("Cannot read a dimension that is prior to the last dimension read")
elseif order_of_dimension_in_cache < order_of_dimension_to_read
if order_of_dimension_in_iterator > order_of_dimension_to_read
for (i, ts) in enumerate(reader.metadata.labels)
reader.all_labels_data_cache[i] = NaN
end
else
while order_of_dimension_in_iterator <= order_of_dimension_to_read
_quiver_next_dimension!(reader)
dimension_in_iterator = _current_dimension_in_iterator(reader)
order_of_dimension_in_iterator = _calculate_order_in_file(reader.metadata, dimension_in_iterator...)
end
end

_quiver_next_dimension!(reader)
return nothing
else
while order_of_dimension_in_iterator <= order_of_dimension_to_read
_quiver_next_dimension!(reader)
dimension_in_iterator = _current_dimension_in_iterator(reader)
order_of_dimension_in_iterator = _calculate_order_in_file(reader.metadata, dimension_in_iterator...)
end
return nothing
end
return nothing
end
Expand Down Expand Up @@ -214,7 +219,7 @@ function convert(

while reader.reader.next !== nothing
Quiver.next_dimension!(reader)
dim_kwargs = OrderedDict(Symbol.(metadata.dimensions) .=> reader.last_dimension_read)
dim_kwargs = OrderedDict(Symbol.(metadata.dimensions) .=> reader.dimension_to_read)
Quiver.write!(writer, reader.data; dim_kwargs...)
end

Expand Down
25 changes: 18 additions & 7 deletions src/reader.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,8 @@ mutable struct Reader{I <: Implementation, R}
reader::R
filename::String
metadata::Metadata
last_dimension_read::Vector{Int}
dimension_in_cache::Vector{Int}
dimension_to_read::Vector{Int}
all_labels_data_cache::Vector{Float32}
data::Vector{Float32}
labels_to_read::Vector{String}
Expand All @@ -12,7 +13,8 @@ mutable struct Reader{I <: Implementation, R}
reader::R,
filename::String,
metadata::Metadata,
last_dimension_read::Vector{Int};
dimension_in_cache::Vector{Int},
dimension_to_read::Vector{Int};
labels_to_read::Vector{String} = metadata.labels,
carrousel::Bool = false,
) where {I, R}
Expand Down Expand Up @@ -40,7 +42,8 @@ mutable struct Reader{I <: Implementation, R}
reader,
filename,
metadata,
last_dimension_read,
dimension_in_cache,
dimension_to_read,
all_labels_data_cache,
data,
labels_to_read,
Expand All @@ -52,17 +55,24 @@ mutable struct Reader{I <: Implementation, R}
end
end

function _build_last_dimension_read!(reader::Reader; dims...)
function _build_dimension_to_read!(reader::Reader; dims...)
for (i, dim) in enumerate(reader.metadata.dimensions)
if reader.carrousel
reader.last_dimension_read[i] = mod1(dims[dim], reader.metadata.dimension_size[i])
reader.dimension_to_read[i] = mod1(dims[dim], reader.metadata.dimension_size[i])
else
reader.last_dimension_read[i] = dims[dim]
reader.dimension_to_read[i] = dims[dim]
end
end
return nothing
end

function _build_dimension_in_cache!(reader::Reader)
for i in 1:reader.metadata.number_of_dimensions
reader.dimension_in_cache[i] = reader.dimension_to_read[i]
end
return nothing
end

function _move_data_from_buffer_cache_to_data!(reader::Reader)
@inbounds for (i, index) in enumerate(reader.indices_of_labels_to_read)
reader.data[i] = reader.all_labels_data_cache[index]
Expand All @@ -72,8 +82,9 @@ end

function goto!(reader::Reader; dims...)
validate_dimensions(reader.metadata, dims...)
_build_last_dimension_read!(reader; dims...)
_build_dimension_to_read!(reader; dims...)
_quiver_goto!(reader)
_build_dimension_in_cache!(reader)
_move_data_from_buffer_cache_to_data!(reader)
return reader.data
end
Expand Down
128 changes: 126 additions & 2 deletions test/test_read_write.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -448,9 +448,127 @@ function read_write_goto_csv_3()
for block in 1:num_blocks
for segment in 1:num_segments_per_block_scenario[block, scenario]
data = [stage, scenario, block + segment]
if stage == scenario == block == segment == 1
Quiver.write!(writer, data; stage, scenario, block, segment)
end
end
end
end

Quiver.close!(writer)

reader = Quiver.Reader{Quiver.csv}(filename)
for stage in 1:num_stages
for scenario in 1:num_scenarios
for block in 1:num_blocks
for segment in 1:max_num_segments
Quiver.goto!(reader; stage, scenario, block, segment)
if all(isnan.(reader.data))
continue
end
@test reader.data == [stage, scenario, block + segment]
end
end
end
end

Quiver.close!(reader)

rm("$filename.$(Quiver.file_extension(Quiver.csv))")
rm("$filename.toml")
end

function read_write_goto_csv_4()
filename = joinpath(@__DIR__, "test_read_goto_csv_4")

initial_date = DateTime(2006, 1, 1)
num_stages = 10
num_scenarios = 12
num_blocks = 24
num_segments_per_block_scenario = [s + b for b in 1:num_blocks, s in 1:num_scenarios]
max_num_segments = maximum(num_segments_per_block_scenario)
num_time_series = 3

dimensions = ["stage", "scenario", "block", "segment"]
labels = ["agent_$i" for i in 1:num_time_series]
time_dimension = "stage"
dimension_size = [num_stages, num_scenarios, num_blocks, max_num_segments]

writer = Quiver.Writer{Quiver.csv}(
filename;
dimensions,
labels,
time_dimension,
dimension_size,
initial_date = initial_date
)

for stage in 1:num_stages
for scenario in 1:num_scenarios
for block in 1:num_blocks
for segment in 1:num_segments_per_block_scenario[block, scenario]
data = [stage, scenario, block + segment]
Quiver.write!(writer, data; stage, scenario, block, segment)
end
end
end
end

Quiver.close!(writer)

reader = Quiver.Reader{Quiver.csv}(filename)
for stage in 1:num_stages
for scenario in 1:num_scenarios
for block in 1:num_blocks
for segment in 1:max_num_segments
Quiver.goto!(reader; stage, scenario, block, segment)
if iseven(scenario)
continue
end
if all(isnan.(reader.data))
continue
end
@test reader.data == [stage, scenario, block + segment]
end
end
end
end

Quiver.close!(reader)

rm("$filename.$(Quiver.file_extension(Quiver.csv))")
rm("$filename.toml")
end

function read_write_goto_csv_5()
filename = joinpath(@__DIR__, "test_read_goto_csv_5")

initial_date = DateTime(2006, 1, 1)
num_stages = 1
num_scenarios = 1
num_blocks = 1
num_segments_per_block_scenario = [s + b for b in 1:num_blocks, s in 1:num_scenarios]
max_num_segments = maximum(num_segments_per_block_scenario)
num_time_series = 3

dimensions = ["stage", "scenario", "block", "segment"]
labels = ["agent_$i" for i in 1:num_time_series]
time_dimension = "stage"
dimension_size = [num_stages, num_scenarios, num_blocks, max_num_segments]

writer = Quiver.Writer{Quiver.csv}(
filename;
dimensions,
labels,
time_dimension,
dimension_size,
initial_date = initial_date
)

for stage in 1:num_stages
for scenario in 1:num_scenarios
for block in 1:num_blocks
for segment in 1:num_segments_per_block_scenario[block, scenario]
data = [stage, scenario, block + segment]
Quiver.write!(writer, data; stage, scenario, block, segment)
end
end
Expand All @@ -460,7 +578,11 @@ function read_write_goto_csv_3()
Quiver.close!(writer)

reader = Quiver.Reader{Quiver.csv}(filename)
@test_throws ErrorException Quiver.goto!(reader; stage = 1, scenario = 1, block = 1, segment = 1)
stage = scenario = block = segment = 1
Quiver.goto!(reader; stage, scenario, block, segment)
@test reader.data == [stage, scenario, block + segment]
Quiver.goto!(reader; stage, scenario, block, segment)
@test reader.data == [stage, scenario, block + segment]

Quiver.close!(reader)

Expand Down Expand Up @@ -1014,6 +1136,8 @@ function test_read_write_implementations()
read_write_goto_csv_1()
read_write_goto_csv_2()
read_write_goto_csv_3()
read_write_goto_csv_4()
read_write_goto_csv_5()
end
end
end
Expand Down

4 comments on commit f9112c2

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Registration pull request created: JuliaRegistries/General/115315

Tip: Release Notes

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"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
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Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.1.5 -m "<description of version>" f9112c2350019ec583d291a3970860db5521dc95
git push origin v0.1.5

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Registration pull request updated: JuliaRegistries/General/115315

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.1.5 -m "<description of version>" f9112c2350019ec583d291a3970860db5521dc95
git push origin v0.1.5

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