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dasludaslu
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Merge pull request #97 from ClojureCivitas/hrv-for-macroexpand-noj
Hrv for macroexpand noj
2 parents 30f9c69 + 27c17ea commit e350991

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‎site/data_analysis/heart_rate_variability/exploring_heart_rate_variability.qmd‎

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‎src/data_analysis/heart_rate_variability/exploring_heart_rate_variability.clj‎

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@@ -27,7 +27,7 @@
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[java-time.api :as jt]))
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;; # Exploring HRV
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;; # Exploring HRV - DRAFT 🛠
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(ns data-analysis.heart-rate-variability.exploring-heart-rate-variability
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(:require [tech.v3.datatype :as dtype]
@@ -75,8 +75,7 @@
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(plotly/layer-bar {:=y :ppi})))
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(def compute-spectrograms
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(def compute-measures
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(fn [ppi-ds {:keys [sampling-rate
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window-size-in-sec ]}]
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(let [spline (interp/interpolation
@@ -96,13 +95,23 @@
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hop-size 8
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n-windows (int (/ (- n window-size)
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hop-size))
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spectrograms (->> (range n-windows)
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(pfor/pmap (fn [w]
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(let [start-idx (* w hop-size)
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window (-> resampled-ppi
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:ppi
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(dtype/sub-buffer start-idx window-size))
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window-standardized (stats/standardize window)
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windows (->> (range n-windows)
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(map (fn [w]
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[w (let [start-idx (* w hop-size)]
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(-> resampled-ppi
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:ppi
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(dtype/sub-buffer start-idx window-size)))])))
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rmssds (->> windows
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(map (fn [[w window]]
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(-> window
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(tcc/shift 1)
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(tcc/- window)
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tcc/sq
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tcc/mean
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tcc/sqrt))))
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spectrograms (->> windows
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(pfor/pmap (fn [[w window]]
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(let [window-standardized (stats/standardize window)
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window-filtered (.bandPassFilter bw
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(double-array window-standardized)
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4
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vec)]
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{:sampling-rate sampling-rate
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:resampled-ppi resampled-ppi
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:rmssds rmssds
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:spectrograms spectrograms})))
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(comment
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(compute-spectrograms my-ppi
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{:sampling-rate 10
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:window-size-in-sec 60}))
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(compute-measures my-ppi
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{:sampling-rate 10
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:window-size-in-sec 60}))
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;; [An Overview of Heart Rate Variability Metrics and Norms](https://pmc.ncbi.nlm.nih.gov/articles/PMC5624990/)
@@ -145,63 +154,70 @@
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tcc/sum))))
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(defn plot-with-power-spectrum [{:keys [sampling-rate
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resampled-ppi
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spectrograms]}]
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(defn plot-with-measures [{:keys [sampling-rate
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resampled-ppi
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rmssds
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spectrograms]}]
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(when spectrograms
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(kind/fragment
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(let [n (-> spectrograms first :magnitude count)
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Nyquist-freq (/ sampling-rate 2.0)
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freq-resolution (/ Nyquist-freq n)
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times (map (comp str :t) spectrograms)
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freqs (tcc/* (range n)
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freq-resolution)]
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[(-> resampled-ppi
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-bar (merge {:=x :t
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:=y :ppi}
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(when (:label resampled-ppi)
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{:=color :label
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:=color-type :nominal}))))
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(kind/plotly
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{:data [{:x times
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:y freqs
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:z (-> (mapv :magnitude spectrograms)
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(tensor/transpose [1 0]))
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:type :heatmap
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:showscale false}]
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:layout {:height 300
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:width 700
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:margin {:t 25}
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:xaxis {:title {:text "t"}}
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:yaxis {:title {:text "freq"}}}})
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(-> {:freq freqs
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:mean-power (-> spectrograms
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(->> (map :magnitude))
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tensor/->tensor
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(tensor/reduce-axis dfn/mean 0))}
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tc/dataset
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-bar {:=x :freq
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:=y :mean-power}))
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(-> {:t times
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:LF-to-HF (->> spectrograms
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(map (partial LF-to-HF freqs)))}
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tc/dataset
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-line {:=x :t
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:=y :LF-to-HF})
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plotly/plot
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(assoc-in [:layout :yaxis :range] [0 4])
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(assoc-in [:layout :yaxis :title] {:text "LF/HF"}))]))))
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(let [n (-> spectrograms first :magnitude count)
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Nyquist-freq (/ sampling-rate 2.0)
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freq-resolution (/ Nyquist-freq n)
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times (map (comp str :t) spectrograms)
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freqs (tcc/* (range n)
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freq-resolution)]
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{:resampled-ppi (-> resampled-ppi
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-bar (merge {:=x :t
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:=y :ppi}
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(when (:label resampled-ppi)
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{:=color :label
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:=color-type :nominal}))))
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:rmssd (-> {:t times
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:rmssd rmssds}
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tc/dataset
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-line {:=x :t
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:=y :rmssd})
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plotly/plot
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(assoc-in [:layout :yaxis :range] [0 0.1]))
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:power-spectrum (kind/plotly
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{:data [{:x times
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:y freqs
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:z (-> (mapv :magnitude spectrograms)
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(tensor/transpose [1 0]))
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:type :heatmap
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:showscale false}]
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:layout {:height 300
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:width 700
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:margin {:t 25}
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:xaxis {:title {:text "t"}}
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:yaxis {:title {:text "freq"}}}})
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:mean-power-spectrum (-> {:freq freqs
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:mean-power (-> spectrograms
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(->> (map :magnitude))
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tensor/->tensor
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(tensor/reduce-axis dfn/mean 0))}
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tc/dataset
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-bar {:=x :freq
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:=y :mean-power}))
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:LF-to-HF-series (-> {:t times
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:LF-to-HF (->> spectrograms
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(map (partial LF-to-HF freqs)))}
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tc/dataset
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(plotly/base {:=height 300 :=width 700})
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(plotly/layer-line {:=x :t
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:=y :LF-to-HF})
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plotly/plot
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(assoc-in [:layout :yaxis :range] [0 4])
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(assoc-in [:layout :yaxis :title] {:text "LF/HF"}))})))
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(delay
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(-> my-ppi
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(compute-spectrograms {:sampling-rate 10
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:window-size-in-sec 60})
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plot-with-power-spectrum))
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(compute-measures {:sampling-rate 10
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:window-size-in-sec 60})
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plot-with-measures))
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;; ## Analysing ECG data
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(tcc/shift (:t %) 1)))
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(tc/drop-rows [0]))))
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;; ### Plotting the PPI
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(delay
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(plotly/layer-bar {:=x :t
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:=y :ppi})))
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;; ## Spectrograms again
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;; ### Measures again
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(def WESAD-spectrograms
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(memoize
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(fn [{:keys [ppi-params spectrogram-params]}]
363+
(fn [{:keys [ppi-params measures-params]}]
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(-> ppi-params
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extract-ppi
351-
(compute-spectrograms spectrogram-params)))))
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(compute-measures measures-params)))))
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(delay
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(-> {:ppi-params {:subject-id 5
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:row-interval [0 1000000]}
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:spectrogram-params {:sampling-rate 10
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:window-size-in-sec 120}}
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:measures-params {:sampling-rate 10
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:window-size-in-sec 120}}
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WESAD-spectrograms
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plot-with-power-spectrum))
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plot-with-measures))
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;; ## A subject's journey
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(def id->label
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[:transient, :baseline,
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:stress, :amusement, :meditation,
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:ignore :ignore :ignore])
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(def label-intervals
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(memoize
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(fn [subject]
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(-> (labelled-dataset subject)
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:label
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(->> (partition-by identity)
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(map (fn [part]
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[(-> part first int id->label)
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(count part)])))
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tc/dataset
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(tc/rename-columns [:label :n])
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(tc/add-column :offset #(cons 0 (reductions + (:n %))))
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(tc/select-columns [:offset :n :label])))))
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(delay
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(label-intervals 5))
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(delay
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(let [subject 5]
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(kind/fragment
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(-> (label-intervals subject)
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(tc/select-rows #(not= (:label %) :ignore))
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#_(tc/select-rows #(= (:label %) :meditation))
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(tc/rows :as-maps)
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(->> (mapcat (fn [{:keys [offset n label]}]
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[label
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(try (-> {:ppi-params {:subject-id subject
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:row-interval [offset (+ offset n)]}
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:measures-params {:sampling-rate 10
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:window-size-in-sec 120}}
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WESAD-spectrograms
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plot-with-measures)
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(catch Exception e 'unavailable))])))))))

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