gin commit from red

New files: 267
Modified files: 1

README.md

@@ -1,3 +1,48 @@
-# Su_et_al_2023_OriRefRepulsion
+This repository contains the code and data for the manuscript "Reference induces biases in late visual processing".
+
+
+## Codes
+The programming requires Psychopy (ideally v2020.1 or newer versions) and Python 3.7.
+
+## File structure
+
+```
+Directory 
+│
+|
+└───config
+|   |   monitor_settings_VPixx.yaml     # monitor settings of VPixx
+|   |   config.yaml                     # experiment configuration
+|   |   params_noise_mix.yaml           # experiment stimulus parameter 
+│   └───
+|
+└───data
+|   |   dat.csv                         # all data for the main experiment 
+|   |   dat_E_rep.csv                   # supplementary data (dual-task condition, reference was presented throughout the whole trial)
+|   |   dat_I_rep.csv                   # supplementary data (singal-task condition)
+│   └───s00                             # directory for data of subject s00
+|       |  s00.yaml                     # subject activity log YAML file, as a record of all blocks
+│       └───raw_data
+|           └───s00_20200000T0000.yaml  # single block raw data YAML
+|
+└───exp                                 # directory for scripts for experiments
+|   |   exp.py                          # experiment script  
+|   |   write_data.py                   # write data to YAML files
+|   └── 
+|
+└───data analysis                       # directory for data analysis scripts and results
+|   |   load_data.py                    # read and load data from YAML files
+|   |   curvefit_mixgamma               # directory for distribution fitting results
+|   |   recover_model_diff_weightf.py   # modeling script
+|   |   recover_model_v4                # directory for modeling results
+|   └───
+|
+└───manuscript                          # directory for manuscript
+|   |   figures                         # directory for manuscript raw figures
+|   |   MFigures                        # directory for manuscript final figures
+|   └── 
+|
+└───plot_manuscript_figures.ipynb       # Jupyter notebook for plotting manuscript figures
+
+```
 
-Datasets and codes of "Reference induces biases in late visual processing"

config/configs.yaml

@@ -0,0 +1,113 @@
+monitor_settings_file: config/monitor_settings_VPixx.yaml
+#monitor_settings_file: config/monitor_settings_mbp.yaml
+#monitor_settings_file: config/monitor_settings_dell.yaml
+
+window_cfg:
+  units: deg
+  colorSpace: rgb
+
+fix:
+  pos: [0, 0]
+  radius: 0.2
+  lineWidth: 0
+  fillColor: [1, 1, 1]
+
+stimulus:
+  show_time: 0.5
+  RT_limit: 8
+
+judge_cue:
+  pos: [0, 0]
+  radius: 0.2
+  lineWidth: 0
+  fillColor: [-1, -1, -1]
+
+stimulus_oval:
+  pos: [0, 0]
+  size: [0.75, 6.0]
+#  size: [2.5, 6.0]
+  lineWidth: 0
+  fillColor: [0.5, 0.5, 0.5]
+
+stimulus_grating:
+  pos: [0, 0]
+#  size: [0.75, 6.0]
+  size: [6.0, 6.0]
+  contrast: 0.5
+  frequency: 1
+  opacity: 1
+
+stimulus_array:
+  fieldShape: circle
+  pos: [ 0, 0 ]
+  colors: [0.5, 0.5, 0.5]
+  elementSize: [0.8, 0.1]
+  elementMask: circle
+  element_nmb: 24
+  xys_var: 0.1
+  outer:
+    fieldSize: 2.5
+    element_nmb: 16
+  inner:
+    fieldSize: 1.0
+    element_nmb: 8
+
+refline:
+  pos: [0, 0]
+#  size: [18.0, 1.0]
+  lineWidth: 3
+  length: 10
+  lineColor: [-0.5, -0.5, -0.5]
+  RT_limit: 4
+  adapt_time: 0.75
+  multi_lineColor: [-0.2, -0.2, -0.2]
+
+# # For reference line as rectangle
+#refline:
+#  pos: [0, 0]
+#  size: [18.0, 0.1]
+#  lineWidth: 0
+##  fillColor: [0.5, 0.5, 0.5]
+#  fillColor: [-0.5, -0.5, -0.5]
+#  RT_limit: 4
+#  adapt_time: 0.75
+
+refdot:
+  radius: 0.2
+  lineWidth: 0
+  fillColor: [0.5, 0.5, 0.5]
+
+gray_disc:
+  pos: [0, 0]
+  radius: 5.0
+  fillColor: [0, 0, 0]
+  lineWidth: 0
+  edges: 100
+
+mask_stimulus:
+  pos: [0, 0]
+  size:  [10.0, 10.0]
+  contrast: 0.5
+  frequency: 0.03
+  show_time: 0.5
+
+mask_ref:
+  pos: [0, 0]
+  size:  [15.0, 15.0]
+  contrast: 0.5
+  frequency: 0.03
+  show_time: 0.5
+
+ITI: 0.5
+
+text:
+  height: 0.8
+  color: [-1, -1, -1]
+
+probe:
+  pos: [0, 0]
+  length: 3.0
+  lineWidth: 3
+  lineColor: [0.5, 0.5, 0.5]
+
+shape_edges: 100

config/monitor_settings_VPixx.yaml

@@ -0,0 +1,36 @@
+id: DisplayPort-0
+name: ViewPixx Lite 2000A
+vendor: VPixx
+serial: 2804477
+year: 2001
+size:
+ width: 484
+ height: 302
+preferred_mode:
+  width: 1920
+  height: 1200
+  refresh: 120
+  distance: 57
+  color-depth: [10, 10, 10]
+settings:
+  contrast: 95
+  brightness: 50
+  left-right: 55
+  left-right-size: 67
+  up-down: 49
+  up-down-size: 49
+  geo-tilt: 51
+  geo-sym-curve: 35
+  geo-asym-curve: 49
+  geo-trapez: 50
+  gep-parallello: 53
+  kvg-left-right: 53
+  kvg-up-down: 53
+  kvg-up-down-up: 53
+  kvg-up-down-down: 56
+  color-purity-top-right: 50
+  color-purity-top-left: 50
+  color-purity-bottom-left: 50
+  color-purity-bottom-right: 50
+  color-type: simple
+  color-temperature: 7200K

config/params_noise_mix.yaml

@@ -0,0 +1,3 @@
+refline_orientations: [15, 45, 75, 105, 135, 165]
+stimulus_relative_orientations: [-18, -15, -12, -9, -6, -3, 0, 3, 6, 9, 12, 15, 18]
+noise: [0, 9]

data/s2/raw_data/s2_20230316T1733.yaml

@@ -0,0 +1,201 @@
+time: 20230316T1733
+cfg_file: config/configs.yaml
+par_file: config/params_noise_mix.yaml
+monitor_settings_file: config/monitor_settings_VPixx.yaml
+window_cfg:
+  units: deg
+  colorSpace: rgb
+fix:
+  pos:
+  - 0
+  - 0
+  radius: 0.2
+  lineWidth: 0
+  fillColor:
+  - 1
+  - 1
+  - 1
+stimulus:
+  show_time: 0.5
+  RT_limit: 8
+judge_cue:
+  pos:
+  - 0
+  - 0
+  radius: 0.2
+  lineWidth: 0
+  fillColor:
+  - -1
+  - -1
+  - -1
+stimulus_oval:
+  pos:
+  - 0
+  - 0
+  size:
+  - 0.75
+  - 6.0
+  lineWidth: 0
+  fillColor:
+  - 0.5
+  - 0.5
+  - 0.5
+stimulus_grating:
+  pos:
+  - 0
+  - 0
+  size:
+  - 6.0
+  - 6.0
+  contrast: 0.5
+  frequency: 1
+  opacity: 1
+stimulus_array:
+  fieldShape: circle
+  pos:
+  - 0
+  - 0
+  colors:
+  - 0.5
+  - 0.5
+  - 0.5
+  elementSize:
+  - 0.8
+  - 0.1
+  elementMask: circle
+  element_nmb: 24
+  xys_var: 0.1
+  outer:
+    fieldSize: 2.5
+    element_nmb: 16
+  inner:
+    fieldSize: 1.0
+    element_nmb: 8
+refline:
+  pos:
+  - 0
+  - 0
+  lineWidth: 3
+  length: 10
+  lineColor:
+  - -0.5
+  - -0.5
+  - -0.5
+  RT_limit: 4
+  adapt_time: 0.75
+  multi_lineColor:
+  - -0.2
+  - -0.2
+  - -0.2
+refdot:
+  radius: 0.2
+  lineWidth: 0
+  fillColor:
+  - 0.5
+  - 0.5
+  - 0.5
+gray_disc:
+  pos:
+  - 0
+  - 0
+  radius: 5.0
+  fillColor:
+  - 0
+  - 0
+  - 0
+  lineWidth: 0
+  edges: 100
+mask_stimulus:
+  pos:
+  - 0
+  - 0
+  size:
+  - 10.0
+  - 10.0
+  contrast: 0.5
+  frequency: 0.03
+  show_time: 0.5
+mask_ref:
+  pos:
+  - 0
+  - 0
+  size:
+  - 15.0
+  - 15.0
+  contrast: 0.5
+  frequency: 0.03
+  show_time: 0.5
+ITI: 0.5
+text:
+  height: 0.8
+  color:
+  - -1
+  - -1
+  - -1
+probe:
+  pos:
+  - 0
+  - 0
+  length: 3.0
+  lineWidth: 3
+  lineColor:
+  - 0.5
+  - 0.5
+  - 0.5
+shape_edges: 100
+refline_orientations:
+- 15
+- 45
+- 75
+- 105
+- 135
+- 165
+stimulus_relative_orientations:
+- -18
+- -15
+- -12
+- -9
+- -6
+- -3
+- 0
+- 3
+- 6
+- 9
+- 12
+- 15
+- 18
+noise:
+- 0
+- 9
+trial_1:
+  trialCount: 1
+  task_type: 2
+  ref_type: 2
+  stimulus: 87
+  refline: 105
+  relative_stimulus: -18
+  estimate_with_ref: 1
+  noise: 9
+  cw_to_refline: 0
+  RT_refline: 3.17
+  refline_judge_correct: 1
+  response: 91.89
+  bias: 4.89
+  RT_reproduce: 2.23
+  discard_this_trial: false
+trial_2:
+  trialCount: 2
+  task_type: 2
+  ref_type: 2
+  stimulus: 72
+  refline: 75
+  relative_stimulus: -3
+  estimate_with_ref: 1
+  noise: 0
+  cw_to_refline: 1
+  RT_refline: 0.63
+  refline_judge_correct: 0
+  response: 83.79
+  bias: 11.79
+  RT_reproduce: 2.64
+  discard_this_trial: false

data/s2/s2.yaml

@@ -0,0 +1,200 @@
+20220615T1518:
+  block_count: 1
+  block_idx: 20220615T1518
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220615T1518.yaml
+  status: practice
+20220615T1533:
+  block_count: 2
+  block_idx: 20220615T1533
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220615T1533.yaml
+  status: completed
+20220615T1544:
+  block_count: 3
+  block_idx: 20220615T1544
+  block_id_in_session: 1
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220615T1544.yaml
+  status: completed
+20220615T1554:
+  block_count: 4
+  block_idx: 20220615T1554
+  block_id_in_session: 2
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220615T1554.yaml
+  status: completed
+20220615T1604:
+  block_count: 5
+  block_idx: 20220615T1604
+  block_id_in_session: 3
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220615T1604.yaml
+  status: completed
+20220615T1614:
+  block_count: 6
+  block_idx: 20220615T1614
+  block_id_in_session: 4
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220615T1614.yaml
+  status: completed
+20220617T0950:
+  block_count: 7
+  block_idx: 20220617T0950
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T0950.yaml
+  status: practice
+20220617T1008:
+  block_count: 8
+  block_idx: 20220617T1008
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1008.yaml
+  status: completed
+20220617T1029:
+  block_count: 9
+  block_idx: 20220617T1029
+  block_id_in_session: 1
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1029.yaml
+  status: completed
+20220617T1040:
+  block_count: 10
+  block_idx: 20220617T1040
+  block_id_in_session: 2
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1040.yaml
+  status: completed
+20220617T1056:
+  block_count: 11
+  block_idx: 20220617T1056
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1056.yaml
+  status: escape
+20220617T1056:
+  block_count: 12
+  block_idx: 20220617T1056
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1056.yaml
+  status: completed
+20220617T1110:
+  block_count: 12
+  block_idx: 20220617T1110
+  block_id_in_session: 1
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1110.yaml
+  status: completed
+20220617T1138:
+  block_count: 13
+  block_idx: 20220617T1138
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1138.yaml
+  status: completed
+20220617T1148:
+  block_count: 14
+  block_idx: 20220617T1148
+  block_id_in_session: 1
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1148.yaml
+  status: completed
+20220617T1201:
+  block_count: 15
+  block_idx: 20220617T1201
+  block_id_in_session: 2
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1201.yaml
+  status: completed
+20220617T1213:
+  block_count: 16
+  block_idx: 20220617T1213
+  block_id_in_session: 3
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1213.yaml
+  status: completed
+20220617T1223:
+  block_count: 17
+  block_idx: 20220617T1223
+  block_id_in_session: 4
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20220617T1223.yaml
+  status: completed
+20230316T1733:
+  block_count: 18
+  block_idx: 20230316T1733
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1733.yaml
+  status: escape
+20230316T1754:
+  block_count: 19
+  block_idx: 20230316T1754
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1754.yaml
+  status: escape
+20230316T1805:
+  block_count: 20
+  block_idx: 20230316T1805
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1805.yaml
+  status: completed
+20230316T1820:
+  block_count: 21
+  block_idx: 20230316T1820
+  block_id_in_session: 1
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1820.yaml
+  status: completed
+20230316T1835:
+  block_count: 22
+  block_idx: 20230316T1835
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1835.yaml
+  status: completed
+20230316T1847:
+  block_count: 23
+  block_idx: 20230316T1847
+  block_id_in_session: 1
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1847.yaml
+  status: completed
+20230316T1857:
+  block_count: 24
+  block_idx: 20230316T1857
+  block_id_in_session: 2
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
+  data_file: data/s2/raw_data/s2_20230316T1857.yaml
+  status: completed

data/s4/raw_data/s4_20220706T1045.yaml

@@ -0,0 +1,185 @@
+time: 20220706T1045
+cfg_file: config/configs.yaml
+par_file: config/params_noise_mix.yaml
+monitor_settings_file: config/monitor_settings_VPixx.yaml
+window_cfg:
+  units: deg
+  colorSpace: rgb
+fix:
+  pos:
+  - 0
+  - 0
+  radius: 0.2
+  lineWidth: 0
+  fillColor:
+  - 1
+  - 1
+  - 1
+stimulus:
+  show_time: 0.5
+  RT_limit: 8
+judge_cue:
+  pos:
+  - 0
+  - 0
+  radius: 0.2
+  lineWidth: 0
+  fillColor:
+  - -1
+  - -1
+  - -1
+stimulus_oval:
+  pos:
+  - 0
+  - 0
+  size:
+  - 0.75
+  - 6.0
+  lineWidth: 0
+  fillColor:
+  - 0.5
+  - 0.5
+  - 0.5
+stimulus_grating:
+  pos:
+  - 0
+  - 0
+  size:
+  - 6.0
+  - 6.0
+  contrast: 0.5
+  frequency: 1
+  opacity: 1
+stimulus_array:
+  fieldShape: circle
+  pos:
+  - 0
+  - 0
+  colors:
+  - 0.5
+  - 0.5
+  - 0.5
+  elementSize:
+  - 0.8
+  - 0.1
+  elementMask: circle
+  element_nmb: 24
+  xys_var: 0.1
+  outer:
+    fieldSize: 2.5
+    element_nmb: 16
+  inner:
+    fieldSize: 1.0
+    element_nmb: 8
+refline:
+  pos:
+  - 0
+  - 0
+  lineWidth: 3
+  length: 10
+  lineColor:
+  - -0.5
+  - -0.5
+  - -0.5
+  RT_limit: 4
+  adapt_time: 0.75
+  multi_lineColor:
+  - -0.2
+  - -0.2
+  - -0.2
+refdot:
+  radius: 0.2
+  lineWidth: 0
+  fillColor:
+  - 0.5
+  - 0.5
+  - 0.5
+gray_disc:
+  pos:
+  - 0
+  - 0
+  radius: 5.0
+  fillColor:
+  - 0
+  - 0
+  - 0
+  lineWidth: 0
+  edges: 100
+mask_stimulus:
+  pos:
+  - 0
+  - 0
+  size:
+  - 10.0
+  - 10.0
+  contrast: 0.5
+  frequency: 0.03
+  show_time: 0.5
+mask_ref:
+  pos:
+  - 0
+  - 0
+  size:
+  - 15.0
+  - 15.0
+  contrast: 0.5
+  frequency: 0.03
+  show_time: 0.5
+ITI: 0.5
+text:
+  height: 0.8
+  color:
+  - -1
+  - -1
+  - -1
+probe:
+  pos:
+  - 0
+  - 0
+  length: 3.0
+  lineWidth: 3
+  lineColor:
+  - 0.5
+  - 0.5
+  - 0.5
+shape_edges: 100
+refline_orientations:
+- 15
+- 45
+- 75
+- 105
+- 135
+- 165
+stimulus_relative_orientations:
+- -18
+- -15
+- -12
+- -9
+- -6
+- -3
+- 0
+- 3
+- 6
+- 9
+- 12
+- 15
+- 18
+noise:
+- 0
+- 9
+trial_1:
+  trialCount: 1
+  task_type: 1
+  ref_type: 2
+  stimulus: 90
+  refline: 75
+  relative_stimulus: 15
+  estimate_with_ref: 1
+  noise: 0
+  cw_to_refline: null
+  RT_refline: null
+  refline_judge_correct: null
+  response: 18.1
+  bias: -71.9
+  RT_reproduce: 1.51
+  discard_this_trial: true

data/s4/s4.yaml

@@ -0,0 +1,104 @@
+20220706T0854:
+  block_count: 1
+  block_idx: 20220706T0854
+  block_id_in_session: 0
+  cfg_file: config/configs.yaml
+  par_file: config/params_noise_mix.yaml
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data/s4/s4_1st.yaml

@@ -0,0 +1,64 @@
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data/s6/s6.yaml

@@ -0,0 +1,184 @@
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data/s7/s7.yaml

@@ -0,0 +1,96 @@
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data/s8/s8.yaml

@@ -0,0 +1,104 @@
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