From dd6d353d81b041a44ce38d5ee78e7d7470fbfeb8 Mon Sep 17 00:00:00 2001
From: agchesebro <76024790+agchesebro@users.noreply.github.com>
Date: Tue, 24 Sep 2024 14:01:09 -0400
Subject: [PATCH 1/3] Batch resampling of a whole dataset

---
 .../RF_processing_saved_voltages.jl                  | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/examples/flattening_circuit/RF_processing_saved_voltages.jl b/examples/flattening_circuit/RF_processing_saved_voltages.jl
index 3e0f9913..db0a2cb9 100644
--- a/examples/flattening_circuit/RF_processing_saved_voltages.jl
+++ b/examples/flattening_circuit/RF_processing_saved_voltages.jl
@@ -22,5 +22,15 @@ function resample_timeseries(data, dt=1)
     return new_data
 end 
 
+orig_sim_path = "/Users/achesebro/Downloads/all_sims/orig_sims/"
+resampled_sim_path = "/Users/achesebro/Downloads/all_sims/resampled_sims/"
 
-data = DataFrame(CSV.File("/Users/achesebro/Downloads/all_sims/sol_trial_1.csv"))
+all_files = readdir(orig_sim_path)
+for i ∈ eachindex(all_files)
+    orig_path = orig_sim_path * all_files[i]
+    resampled_path = resampled_sim_path * all_files[i]
+    orig_data = DataFrame(CSV.File(orig_path))
+    collapse_data = collapse_timesteps(orig_data)
+    resampled_data = resample_timeseries(collapse_data, 1)
+    CSV.write(resampled_path, resampled_data)
+end
\ No newline at end of file

From 87015b68a4bc86ba4f9e82086ff62f97bdd91d54 Mon Sep 17 00:00:00 2001
From: agchesebro <76024790+agchesebro@users.noreply.github.com>
Date: Tue, 24 Sep 2024 15:56:32 -0400
Subject: [PATCH 2/3] Create concatenated time series to convert to fMRI

---
 .../RF_processing_saved_voltages.jl             | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/examples/flattening_circuit/RF_processing_saved_voltages.jl b/examples/flattening_circuit/RF_processing_saved_voltages.jl
index db0a2cb9..e770278e 100644
--- a/examples/flattening_circuit/RF_processing_saved_voltages.jl
+++ b/examples/flattening_circuit/RF_processing_saved_voltages.jl
@@ -33,4 +33,19 @@ for i ∈ eachindex(all_files)
     collapse_data = collapse_timesteps(orig_data)
     resampled_data = resample_timeseries(collapse_data, 1)
     CSV.write(resampled_path, resampled_data)
-end
\ No newline at end of file
+end
+
+concat_file_path = "/Users/achesebro/Downloads/all_sims/concatenated_sims.csv"
+all_files = readdir(resampled_sim_path)
+first_data = DataFrame(CSV.File(resampled_sim_path * all_files[1]))
+all_data = first_data
+
+for i ∈ 2:lastindex(all_files)
+    next_data = DataFrame(CSV.File(resampled_sim_path * all_files[i]))
+    all_data = vcat(all_data, next_data)
+end
+
+new_t = 0:lastindex(all_data.t)-1
+all_data.t .= collect(new_t)
+
+CSV.write(concat_file_path, all_data)
\ No newline at end of file

From ed0fe5a8f5ac43a2d41a22c73d1b56aba7b1f6b1 Mon Sep 17 00:00:00 2001
From: agchesebro <76024790+agchesebro@users.noreply.github.com>
Date: Wed, 16 Oct 2024 14:30:42 -0400
Subject: [PATCH 3/3] Extra helper functions

---
 .../RF_processing_saved_voltages.jl           | 26 ++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/examples/flattening_circuit/RF_processing_saved_voltages.jl b/examples/flattening_circuit/RF_processing_saved_voltages.jl
index e770278e..6dc246f6 100644
--- a/examples/flattening_circuit/RF_processing_saved_voltages.jl
+++ b/examples/flattening_circuit/RF_processing_saved_voltages.jl
@@ -48,4 +48,28 @@ end
 new_t = 0:lastindex(all_data.t)-1
 all_data.t .= collect(new_t)
 
-CSV.write(concat_file_path, all_data)
\ No newline at end of file
+CSV.write(concat_file_path, all_data)
+
+all_data = CSV.read(concat_file_path, DataFrame)
+
+using DSP, Distributions, StatsBase
+
+function HRF(x,rtu=6.0,δ1=6.0,δ2=16.0,τ1=1.0,τ2=1.0,C=0.0)
+    return pdf.(Gamma(δ1,τ1),x)-pdf.(Gamma(δ2,τ2),x)/rtu + C
+end
+
+
+t_hrf = 0:0.001:32
+hrf = HRF.(t_hrf)
+
+hrf_data = DataFrame()
+
+for i ∈ names(all_data)[2:end]
+    next_data = all_data[:, i]
+    next_data = StatsBase.transform(fit(UnitRangeTransform, next_data), next_data)
+    conv_data = conv(next_data, hrf)
+    hrf_data[!, i] = conv_data
+end
+
+hrf_path = "/Users/achesebro/Downloads/all_sims/hrf_sims.csv"
+CSV.write(hrf_path, hrf_data)