Remove explicit dependency on HDF5

Project.toml

@@ -10,7 +10,6 @@ DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 ElasticArrays = "fdbdab4c-e67f-52f5-8c3f-e7b388dad3d4"
-HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 LegendDataManagement = "9feedd95-f0e0-423f-a8dc-de0970eae6b3"
@@ -48,7 +47,6 @@ DSP = "0.7"
 DelimitedFiles = "1"
 Distributions = "0.23, 0.24, 0.25"
 ElasticArrays = "1"
-HDF5 = "0.15, 0.16, 0.17"
 IntervalSets = "0.5, 0.6, 0.7"
 JSON = "0.21"
 LegendDataManagement = "0.2.1, 0.3, 0.4"

docs/Project.toml

@@ -1,6 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
 LegendHDF5IO = "c9265ca6-b027-5446-b1a4-febfa8dd10b0"
 LegendTestData = "33d6da08-6349-5f7c-b5a4-6ff4d8795aaf"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"

docs/src/tutorials/simulate_ideal_pulses_lit.jl

@@ -78,14 +78,13 @@ plot(pss_table.waveform[1:5], legend=false, title="only p+ contact pulses")
 
 # You can save simulated pulses in a file that can be used later.
 
-using HDF5
 using LegendHDF5IO
 
 #
 
 pss_name = "cache/test_100wfs_pss.hdf5"
-h5open(pss_name, "w") do f
-    LegendHDF5IO.writedata(f, "pss/pss", pss_table[1:5])
-    LegendHDF5IO.writedata(f, "pss/truth", pss_truth[1:5])
+lh5open(pss_name, "w") do f
+    LegendHDF5IO.writedata(f.data_store, "pss/pss", pss_table[1:5])
+    LegendHDF5IO.writedata(f.data_store, "pss/truth", pss_truth[1:5])
 end
 

docs/src/tutorials/simulate_realistic_waveforms_lit.jl

@@ -96,14 +96,13 @@ plot(raw_table.waveform[1:10], legend=false, title="only p+ contact waveforms")
 
 # You can save simulated waveforms in a file that can be used later
 
-using HDF5
 using LegendHDF5IO
 
 #
 
 raw_name = "cache/test_100wfs_raw.hdf5"
-h5open(raw_name, "w") do f
-    LegendHDF5IO.writedata(f, "raw", raw_table[1:10])
+lh5open(raw_name, "w") do f
+    LegendHDF5IO.writedata(f.data_store, "raw", raw_table[1:10])
 end
 
 # ## Simulate from `pss` table in code
@@ -131,14 +130,13 @@ plot(
 # Save the pss file for the next section
 
 using LegendHDF5IO
-using HDF5
 
 #
 
 pss_name = "cache/test_100wfs_pss.hdf5"
-h5open(pss_name, "w") do f
-    LegendHDF5IO.writedata(f, "pss/pss", pss_table[1:10])
-    LegendHDF5IO.writedata(f, "pss/truth", pss_truth[1:10])
+lh5open(pss_name, "w") do f
+    LegendHDF5IO.writedata(f.data_store, "pss/pss", pss_table[1:10])
+    LegendHDF5IO.writedata(f.data_store, "pss/truth", pss_truth[1:10])
 end
 
 # ## Simulate from pre-saved `pss` hdf5 file

src/LegendGeSim.jl

@@ -16,7 +16,6 @@ using DelimitedFiles
 using Distributions
 using DSP 
 using ElasticArrays
-using HDF5
 using IntervalSets
 using JSON
 using LegendDataManagement

src/baselines.jl

@@ -37,16 +37,18 @@ function baseline_catalog(raw_filename::AbstractString)
 
     if isfile(base_filename)
         @info "Selecting baseline samples from $base_filename"
-        baseline_table = h5open(base_filename) do input Table(waveform = LegendDataTypes.readdata(input, "raw/waveform")) end
+        baseline_table = LegendHDF5IO.lh5open(base_filename) do input 
+            Table(waveform = LegendHDF5IO.readdata(input.data_store, "raw/waveform")) 
+        end
     else
         @info "Extracting baseline samples from $raw_filename"  
-        raw_table = HDF5.h5open(raw_filename, "r") do input
-            LegendHDF5IO.readdata(input, "raw")
+        raw_table = LegendHDF5IO.lh5open(raw_filename, "r") do input
+            LegendHDF5IO.readdata(input.data_store, "raw")
         end  
         baseline_table = baseline_catalog(raw_table)
         # cache for later
         if !ispath(dirname(base_filename)) mkpath(dirname(base_filename)) end
-        h5open(base_filename, "w") do f LegendHDF5IO.writedata(f, "raw", baseline_table) end
+        LegendHDF5IO.lh5open(base_filename, "w") do f LegendHDF5IO.writedata(f.data_store, "raw", baseline_table) end
         @info "Baselines saved to $base_filename"
     end
 

src/detector.jl

@@ -107,15 +107,15 @@ function simulate_detector(det_meta::PropDict, env::Environment, simulator::SSDS
             if !ispath(dirname(h5fn))
                 mkpath(dirname(h5fn))
             end
-            HDF5.h5open(h5fn, "w") do h5f
-                LegendHDF5IO.writedata(h5f, "SSD_electric_potential", NamedTuple(sim.electric_potential))
-                LegendHDF5IO.writedata(h5f, "SSD_point_types", NamedTuple(sim.point_types))
-                LegendHDF5IO.writedata(h5f, "SSD_q_eff_fix", NamedTuple(sim.q_eff_fix))
-                LegendHDF5IO.writedata(h5f, "SSD_q_eff_imp", NamedTuple(sim.q_eff_imp))
-                LegendHDF5IO.writedata(h5f, "SSD_dielectric_distribution", NamedTuple(sim.ϵ_r))
-                LegendHDF5IO.writedata(h5f, "SSD_electric_field", NamedTuple(sim.electric_field))
+            LegendHDF5IO.lh5open(h5fn, "w") do h5f
+                LegendHDF5IO.writedata(h5f.data_store, "SSD_electric_potential", NamedTuple(sim.electric_potential))
+                LegendHDF5IO.writedata(h5f.data_store, "SSD_point_types", NamedTuple(sim.point_types))
+                LegendHDF5IO.writedata(h5f.data_store, "SSD_q_eff_fix", NamedTuple(sim.q_eff_fix))
+                LegendHDF5IO.writedata(h5f.data_store, "SSD_q_eff_imp", NamedTuple(sim.q_eff_imp))
+                LegendHDF5IO.writedata(h5f.data_store, "SSD_dielectric_distribution", NamedTuple(sim.ϵ_r))
+                LegendHDF5IO.writedata(h5f.data_store, "SSD_electric_field", NamedTuple(sim.electric_field))
                 for i in eachindex(sim.weighting_potentials)
-                    LegendHDF5IO.writedata(h5f, "SSD_weighting_potential_$(i)", NamedTuple(sim.weighting_potentials[i]))
+                    LegendHDF5IO.writedata(h5f.data_store, "SSD_weighting_potential_$(i)", NamedTuple(sim.weighting_potentials[i]))
                 end
             end
             @info("-> Saved cached simulation to $h5fn")
@@ -125,7 +125,7 @@ function simulate_detector(det_meta::PropDict, env::Environment, simulator::SSDS
         # read from previously cached
         sim = construct_ssd_simulation(det_meta, env, simulator)
         @info("Reading SSD simulation from cached file $h5fn")
-        HDF5.h5open(h5fn, "r") do h5f
+        LegendHDF5IO.lh5open(h5fn, "r") do h5f
             sim.electric_potential = ElectricPotential(LegendHDF5IO.readdata(h5f, "SSD_electric_potential"))
             sim.point_types = PointTypes(LegendHDF5IO.readdata(h5f, "SSD_point_types"))
             sim.q_eff_fix = EffectiveChargeDensity(LegendHDF5IO.readdata(h5f, "SSD_q_eff_fix"))

src/pss_to_raw.jl

@@ -66,9 +66,9 @@ end
 
 # wrapper for user reading from pre-saved pss file
 function pss_to_raw(pss_file::AbstractString, setup_settings::Dict, noise_settings::Dict=Dict("type"=>"none"); n_waveforms::Int=0)
-    pss_h5 = h5open(pss_file, "r")
-    pss_table = LegendHDF5IO.readdata(pss_h5, "pss/pss")
-    pss_truth = LegendHDF5IO.readdata(pss_h5, "pss/truth")
+    pss_h5 = LegendHDF5IO.lh5open(pss_file, "r")
+    pss_table = LegendHDF5IO.readdata(pss_h5.data_store, "pss/pss")
+    pss_truth = LegendHDF5IO.readdata(pss_h5.data_store, "pss/truth")
     close(pss_h5)
 
     pss_to_raw(pss_table, pss_truth,  setup_settings, noise_settings; n_waveforms)

src/stp_to_pss.jl

@@ -30,8 +30,8 @@ end
 
 
 # function stp_to_pss(stp_filepath::AbstractString, det_meta_fullpath::AbstractString, sim_config_filename::AbstractString)
-#     stp_table = h5open(stp_filepath, "r") do input
-#         LegendHDF5IO.readdata(input, "stp")
+#     stp_table = LegendHDF5IO.lh5open(stp_filepath, "r") do input
+#         LegendHDF5IO.readdata(input.data_store, "stp")
 #     end
 
 #     stp_to_pss(stp_table, det_meta_fullpath, sim_config_filename)

test/runtests.jl

@@ -3,7 +3,7 @@
 using Test
 
 using LegendGeSim
-using LegendHDF5IO, HDF5
+using LegendHDF5IO
 using LegendTestData
 using Unitful
 
@@ -62,9 +62,9 @@ end
     end
 
     pss_name = "cache/" * LegendGeSim.filename(path_to_pet_file) * "_pss.hdf5"
-    h5open(pss_name, "w") do f
-        LegendHDF5IO.writedata(f, "pss/pss", pss_table)
-        LegendHDF5IO.writedata(f, "pss/truth", pss_truth)
+    LegendHDF5IO.lh5open(pss_name, "w") do f
+        LegendHDF5IO.writedata(f.data_store, "pss/pss", pss_table)
+        LegendHDF5IO.writedata(f.data_store, "pss/truth", pss_truth)
     end
 
     @testset "pss I/O using LegendHDF5IO" begin