pyNIBS 0.2024.8__py3-none-any.whl → 0.2026.1__py3-none-any.whl

pyNIBS-0.2024.8.dist-info/RECORD

@@ -1,107 +0,0 @@
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pynibs/data/configuration_exp0.yaml

@@ -1,59 +0,0 @@
-########################################################################################################################
-# This configuration file can be used to set values in pynibs.Element() that influence the regression.                 #
-########################################################################################################################
-#
-#
-############################################## General regression concept ##############################################
-# While trying to find the best fit, many possible regression functions are calculated and the best one is picked.
-# Usually, that is the one that explains the most noise, meaning that the data points have a minimal distance to the
-# regression function. The function exp0 always looks like the following term, with varying coefficients x_0 and r:
-##     y = e^{r(x-x_0)}
-##     (r : Slope parameter (steepness))
-##     (x0 : Horizontal shift along the abscissa)
-
-# The usual approach is to start with a function described by some initial values (init_vals) for x_0 and r and try out
-# many other values within the value limits (limits), minimizing the distance between regression function and real data.
-# During refitting, different initial vales (calculated within the random_vals_init_range) are used to see whether a
-# better result can be achieved.
-
-############################################### Picking suitable values ################################################
-# Initial values for the regression coefficients
-init_vals:
-  r: 0.1
-  x0: 10
-# Strategy: Pick the values you may expect the result to have, or that are not far-fetched. Picking reasonable initial
-# values can speed up the fitting procedure.
-
-# Values that limit all possible regression coefficients:
-limits:
-  r:
-  - 1.0e-12
-  - 100
-  x0:
-  - 0
-  - 1000
-# Strategy: Rather wide range recommended, since a few points could have very extreme values and therefore be
-# approximated by a function very different from the expected values. E.g. a multiple of the presented data range.
-# (Note: This should not be used to factor out outliers, since an approximation will still be calculated, but with too
-# narrow limits it will just be a very bad one.)
-
-# Value range for the calculation of new initial values for refits:
-random_vals_init_range:
-  r:
-  - 0
-  - 0.2
-  x0:
-  - 0
-  - 10
-# Strategy: During refitting, new initial values are calculated by picking a random number between these lower and upper
-# bounds, so the range should be a lot smaller than 'limits' and somewhat symmetrical around the 'init_vals'.
-
-
-# Example usage:
-##
-##        configfile = configuration_exp0.yaml
-##        with open(configfile, "r") as yamlfile:
-##            config = yaml.load(yamlfile, Loader=yaml.FullLoader)
-##
-##        pynibs.regress_data(...,
-##                           **configfile)

pynibs/data/configuration_linear_MEP.yaml

@@ -1,61 +0,0 @@
-########################################################################################################################
-# This configuration file can be used to set values in pynibs.Element() that influence the regression.                 #
-# The values in this version are optimized for MEP data.                                                     #
-########################################################################################################################
-#
-#
-############################################## General regression concept ##############################################
-# While trying to find the best fit, many possible regression functions are calculated and the best one is picked.
-# Usually, that is the one that explains the most noise, meaning that the data points have a minimal distance to the
-# regression function. With linear regression, this function always looks like the following term, with varying
-# coefficients m and n:
-##     y = m*x + n
-##     (m is the slope)
-##     (n is the intercept with the y-axis)
-
-# The usual approach is to start with a function described by some initial values (init_vals) for m and n and try out
-# many other values within the value limits (limits), minimizing the distance between regression function and real data.
-# During refitting, different initial vales (calculated within the random_vals_init_range) are used to see whether a
-# better result can be achieved.
-
-############################################### Picking suitable values ################################################
-# Initial values for the regression coefficients:
-init_vals:
-  m: 0.3
-  n: -1
-# Strategy: Pick the values you may expect the result to have, or that are not far-fetched. Picking reasonable initial
-# values can speed up the fitting procedure.
-
-# Values that limit all possible regression coefficients:
-limits:
-  m:
-  - -100
-  - 100
-  n:
-  - -100
-  - 100
-# Strategy: Rather wide range recommended, since a few points could have very extreme values and therefore be
-# approximated by a function very different from the expected values. E.g. a multiple of the presented data range.
-# (Note: This should not be used to factor out outliers, since an approximation will still be calculated, but with too
-# narrow limits it will just be a very bad one.)
-
-# Value range for the calculation of new initial values for refits:
-random_vals_init_range:
-  m:
-  - 0
-  - 100
-  n:
-  - 0
-  - 0.3
-# Strategy: During refitting, new initial values are calculated by picking a random number between these lower and upper
-# bounds, so the range should be a lot smaller than 'limits' and somewhat symmetrical around the 'init_vals'.
-
-
-# Example usage:
-##
-##        configfile = configuration_linear_MEP.yaml
-##        with open(configfile, "r") as yamlfile:
-##            config = yaml.load(yamlfile, Loader=yaml.FullLoader)
-##
-##        pynibs.regress_data(...,
-##                           **configfile)

pynibs/data/configuration_linear_RT.yaml

@@ -1,61 +0,0 @@
-########################################################################################################################
-# This configuration file can be used to set values in pynibs.Element() that influence the regression.                 #
-# The values in this version are optimized for reaction time data.                                                     #
-########################################################################################################################
-#
-#
-############################################## General regression concept ##############################################
-# While trying to find the best fit, many possible regression functions are calculated and the best one is picked.
-# Usually, that is the one that explains the most noise, meaning that the data points have a minimal distance to the
-# regression function. With linear regression, this function always looks like the following term, with varying
-# coefficients m and n:
-##     y = m*x + n
-##     (m is the slope)
-##     (n is the intercept with the y-axis)
-
-# The usual approach is to start with a function described by some initial values (init_vals) for m and n and try out
-# many other values within the value limits (limits), minimizing the distance between regression function and real data.
-# During refitting, different initial vales (calculated within the random_vals_init_range) are used to see whether a
-# better result can be achieved.
-
-############################################### Picking suitable values ################################################
-# Initial values for the regression coefficients:
-init_vals:
-  m: 0.1
-  n: 300
-# Strategy: Pick the values you may expect the result to have, or that are not far-fetched. Picking reasonable initial
-# values can speed up the fitting procedure.
-
-# Values that limit all possible regression coefficients:
-limits:
-  m:
-  - -10000
-  - 10000
-  n:
-  - -30000
-  - 30000
-# Strategy: Rather wide range recommended, since a few points could have very extreme values and therefore be
-# approximated by a function very different from the expected values. E.g. a multiple of the presented data range.
-# (Note: This should not be used to factor out outliers, since an approximation will still be calculated, but with too
-# narrow limits it will just be a very bad one.)
-
-# Value range for the calculation of new initial values for refits:
-random_vals_init_range:
-  m:
-  - -22
-  - 22
-  n:
-  - -50
-  - 500
-# Strategy: During refitting, new initial values are calculated by picking a random number between these lower and upper
-# bounds, so the range should be a lot smaller than 'limits' and somewhat symmetrical around the 'init_vals'.
-
-
-# Example usage:
-##
-##        configfile = configuration_linear_RT.yaml
-##        with open(configfile, "r") as yamlfile:
-##            config = yaml.load(yamlfile, Loader=yaml.FullLoader)
-##
-##        pynibs.regress_data(...,
-##                           **configfile)

pynibs/data/configuration_sigmoid4.yaml

@@ -1,68 +0,0 @@
-########################################################################################################################
-# This configuration file can be used to set values in pynibs.Element() that influence the regression.                 #
-# The values in this version are optimized for MEP data.                                                     #
-########################################################################################################################
-#
-#
-############################################## General regression concept ##############################################
-# While trying to find the best fit, many possible regression functions are calculated and the best one is picked.
-# Usually, that is the one that explains the most noise, meaning that the data points have a minimal distance to the
-# regression function. The function sigmoid4 always looks like the following term, with varying coefficients:
-##     y = y_0 + \frac{amp - y_0}{1+e^{-r(x-x_0)}}
-##     (x0 : Horizontal shift along the abscissa)
-##     (r : Slope parameter (steepness))
-##     (amp : Maximum value the sigmoid converges to)
-##     (y0 : Offset value of the sigmoid)
-# Note: The fourth parameter y0 is the only difference between sigmoid and sigmoid4. It presents the possibility to
-# factor in an offset in y-direction.
-
-# The usual regression approach is to start with a function described by some initial values (init_vals) and try out
-# many other values within the value limits (limits), minimizing the distance between regression function and real data.
-# During refitting, different initial vales (calculated within the random_vals_init_range) are used to see whether a
-# better result can be achieved.
-
-element_params:
-  ############################################### Picking suitable values ################################################
-  # Values transforming the initial regression coefficients:
-  init_vals:
-    x0: # set initial x_0 to rate p of the x-data range
-      p: 0.75
-    r: # slope of tangent over middle of 1/p of the e-range (e.g. 25% = 0.25 = 1/4 -> set p=4)
-      p: 4
-    amp: # amp = y_max * m + t
-      m: 1
-      t: 0
-    y0: # y0 = y_min * m + t
-      m: 1
-      t: 0
-  # Strategy: Pick the values you may expect the result to have, or that are not far-fetched. Picking reasonable initial
-  # values can speed up the fitting procedure.
-
-  # Values that limit all possible regression coefficients:
-  limits:
-    limit_factor: # the initial values get multiplied with "limit_factor" to calculate the limits
-      100
-    y0: # y0 \in [c, y_max * m]
-      c: 1.0e-12
-      m: 1
-  # Strategy: Rather wide range recommended, since a few points could have very extreme values and therefore be
-  # approximated by a function very different from the expected values. E.g. a multiple of the presented data range.
-  # (Note: This should not be used to factor out outliers, since an approximation will still be calculated, but with too
-  # narrow limits it will just be a very bad one.)
-
-  # Value range for the calculation of new initial values for refits:
-  random_vals_init_range:
-    range_factor: # the initial values get multiplied with "range_factor" to calculate this range
-      3
-  # Strategy: During refitting, new initial values are calculated by picking a random number between these lower and upper
-  # bounds, so the range should be a lot smaller than 'limits' and somewhat symmetrical around the 'init_vals'.
-
-
-  # Example usage:
-  ##
-  ##        configfile = configuration_sigmoid4.yaml
-  ##        with open(configfile, "r") as yamlfile:
-  ##            config = yaml.load(yamlfile, Loader=yaml.FullLoader)
-  ##
-  ##        pynibs.regress_data(...,
-  ##                           **configfile)

pynibs/data/network mapping configuration/configuration guide.md

@@ -1,238 +0,0 @@
-# Network detection: Guide to using the configuration files
-
-All settings and parameters relevant in the network detection process can be adjusted via the configuration files.
-Here is a short explanation of the process and the configuration entries. 
-
-## Loading the config file
-
-Using the following code you can add the desired configuration file to your script:
-
-    import yaml
-    # choose file name and path
-    configfile = 'configuration_TEMPLATE.yaml'  
-    config_path = '/data/pt_01756/software/git/pynibs/data/network mapping configuration'
-    # read configfile
-    with open(f'{config_path}/{configfile}', "r") as yamlfile:
-        config = yaml.load(yamlfile, Loader=yaml.FullLoader)
-        print("-" * 64)
-        print("Using file '" + configfile + "' for current parameter setting.")
-        print("-" * 64)
-
-Aside from that, the NDA application and testing functions only need the experimental data (e_matrix, response_values, roi_surf, fn_geo)
-and the base_path (output folder).
-
-## Configuration Parameters Guide
-
-There are two different main functions: `network_detection_algorithm_testing()` and 
-`network_detection_algorithm_application()`. The configuration parameters are very similar, many entries apply to both. 
-They are presented separately in the following for simplicity.
-
-
-### Application (real data)
-
-<u> Binarization </u>
-
-Data binarization is a crucial preprocessing step since it determines what data the algorithm considers as affected.
-Carefully adjust to the data at hand. Note that this is only relevant for the scoring_method 'clf'.
-Default function is `binarize_response_data()`. For MEPs, you could also use `binarize_real_meps()`.
-
-- ``bin_method``: Method used to calculate the binarization threshold.
-  - Options: `'mean'`, `'slope'`, `'median'`.
-
-- ``bin_factor``: Multiplied with the value of `bin_method(response)` is used as binarization threshold. 
-(Above=1=affected, below=0=not affected).
-
-<u> Scoring </u>
-
-- ``scoring_method``: Select the method for the computation of hotspot scores per ROI element. 
-  - Options: `'clf'`, `'regression'`, `'regress_data'` (single hotspot), `'mi'` (single hotspot).
-  - Remark: 
-  Network detection:
-    - `'clf'`: Scores are based on the accuracies of Decision Tree Classifiers of pairwise element combinations. (recommended)
-    - `'regression'`: Scores are the R2-scores of multivariable regression.
-    - `'regress_data'`: Scores are the R2-score of a sigmoidal fit.
-    - `'mi'`: Scores are the mutual information scores of the e-fields and the response variables.
-
-- ``scoring_emag_thr``: Threshold above which elements are scored. 
-More specifically: Per element, the `e_mag_max` as the
-maximum e-field magnitude reached in all zaps indicates how accessible an element is to stimulation (gyral element have
-the highest `e_mag_max`). This parameter is the lower bound for the `e_mag_max` of all scored elements. 
-  - Remark: The higher the threshold, the higher the scored elements are on the cortical ROI.
-
-- ``scoring_interval``: Interval at which elements are scored, determines subsampling resolution.
-  - Remark: `1/scoring_interval` elements are scored. Adjust to balance between computational efficiency and scoring detail.
-
-<u>Detection</u>
-
-- ``acc_thr``: Lower bound for the accuracy (clf) or scores (other scoring methods) of hotspot elements. Below that, 
-an element will not be categorized as hotspot.
-  - Remark: See recommendation sheet``data/network mapping configuration/recommendations_for_accuracy_threshold.md``.
-  For the clf-method, there is a table included recommending accuracy thresholds based on sample size.
-
-- ``corr_thr``: Correlation threshold (upper bound) for hotspot pairs. 
-  - Remark: When a second hotspot candidate too highly 
-  correlates with the first one, it is ignored, to avoid double detection of a single hotspot. Preliminary analyses have 
-  shown that this threshold does not have a lot of impact.
-  - 1: no limitation to how correlated they are, 0: only one hotspot allowed)
- 
-
-<u>Additional Info</u>
-
-- ``note``: Arbitrary string for additional comments or notes.
-
-- ``fn_flag``: String to be mentioned in the output files. (to distinguish)
-
-- ``subject_id``: ID of the subject.
-- ``response_spec``:  Specification (if any) to retrieve the response. (e.g. FDI, APB,...)
-- ``e_field``:  Specification (if any) to retrieve the e-field values. (E_tan, E_mag, E_norm)
-
-
-The remaining 8 entries are not saved in the results overview. Namely the following: 
-
-- ``save_files``:  (boolean) Whether to save hotspot scores and scoremaps as HDF5 files.
-
-- ``write_effect_map``: (boolean) Whether to create an effect map. See more under <u> Effect map </u>.
-
-- ``fn_results``: Filename for the CSV the results/evaluation should be saved in.
-To understand output, see ``output_documentation``.
-
-
-<u> Effect map </u>
-
-If the output should include an effect map (useful for validation), the following parameters should be included.
-
-- ``effect_full``:  The e-field magnitude that approximately needs to be reached to achieve the desired effect (in  µV).
-
-- ``effect_saturation``: The approx. e-field magnitude at which the effect is expected to saturate (in  µV).
-
-The effect map depicts the following: Assuming a network as detected was in effect, where can the effect
-be expected highest/lowest? I.e., where is the response expected to be affected most/least?
-This can be useful during experimental validation. 
-
-<u>Plotting</u> 
-
-- ``plot_std``: (boolean) Whether to plot the response data with color indicating response value, and the e-field values
-of the chosen hotspots on x- and y-axis.
-
-- ``plot_bin``: (boolean) Whether to plot the binarized response data with color indicating response category, 
-and the e-field values of the chosen hotspots on x- and y-axis.
-
-- ``plot_curves``: (boolean) Whether to create two response data scatter plots, one for each chosen hotspot. (e-field 
-magnitudes on x-axis, response on y-axis).
-
-
-### Testing (generated data)
-
-<u> Artificial Data Generation </u>
-
-The response will be generated as if `hotspot_elm0` and `hotspot_elm1` 
-form a network of type `network_type`. See function `create_response_data()` for the detailed process.
-
-- ``hotspot_elm0``:  `[0, n_elms-1]`
-Specify the index of the first hotspot element. 
-
-- ``hotspot_elm1``: `[0, n_elms-1]`
-Specify the index of the second hotspot element.
-
-- ``sample_size``: The desired number of samples. Bounded by the number of available e-fields. 
-If `sample_size` is smaller, e-fields are randomly chosen. 
-(See `create_dummy_binary_data.py` for more elaborate e-field choosing functions.)
-
-- ``rn_seed``: Seed for all processes that are in some way random, ensuring reproducibility.
-
-- ``distribution_type``: Defines the statistical distribution type for data generation.
-  - Options: `'normal'`, `'logistic'`.  
-  - Remark: `'ExGaussian'` is also an option but is not fully implemented. 
-
-- ``network_type``: Choose the network the two hotspots are forming. 
-  - Options: `['NO', 'AND', '1_INH_0', 'SH_0', '0_INH_1', 'SH_1', 'XOR', 'OR']`.
-  - Remark:
-    - (1) NO: No network ("pseudonetwork").
-    - (2) AND: Dual node network: Effect if elm0 AND elm1 are stimulated.
-    - (3) 1_INH_0: Dual node network: elm1 inhibits elm0, elm0 has an effect.
-    - (4) SH_0: Single hotspot: Only elm0 has an effect.
-    - (5) 0_INH_1: Dual node network: elm0 inhibits elm1, elm1 has an effect.
-    - (6) SH_1: Single hotspot: Only elm1 has an effect.
-    - (7) XOR: Dual node network: elm0 inhibits elm1, elm1 inhibits elm0. Both have an effect.
-    - (8) OR: Dual node network: Effect if either elm0 or elm1 is stimulated.
-
-- ``effect_full``: E-field magnitude at which the desired effect fully manifests.
-  - Remark: What value makes sense here strongly depends on the range of the e-field values. 
-  For normalized e-field values (1% stimulator intensity) across the motor cortex, values tend to range up to 1.6 µV. 
-  We chose to normalize the effect to 0.9 µV.
-
-- ``effect_saturation``: E-field magnitude at which the desired effect saturates.
-  - Remark: See `effect_full`. We chose an effect saturation at 1.2 µV.
-
-- ``jitter_ratio``: Percentage of data receiving random response values (uniformly distributed within the expected range).
-
-- ``jitter_scale``: Multiplied with the mean value to calculate distribution deviation. Note that a heteroscedastic 
-distribution is implemented at the moment -> the higher the effect, the higher the deviation. 
-
-
-<u> Binarization </u>
-
-Data binarization is a crucial preprocessing step since it determines what data the algorithm considers as affected.
-Carefully adjust to the data at hand.
-Default function is `binarize_response_data()`. For MEPs, you could also use `binarize_real_meps()`.
-
-- ``bin_method``: Method used to calculate the binarization threshold.
-  - Options: `'mean'`, `'slope'`, `'median'`.
-
-- ``bin_factor``: Multiplied with the value of `bin_method(response)` is used as binarization threshold. 
-(Above=1=affected, below=0=not affected).
-
-<u> Scoring </u>
-
-- ``scoring_method``: Select the method for the computation of hotspot scores per ROI element. 
-  - Options: `'clf'`, `'regression'`, `'regress_data'` (single hotspot), `'mi'` (single hotspot).
-  - Remark: 
-  Network detection:
-    - `'clf'`: Scores are based on the accuracies of Decision Tree Classifiers of pairwise element combinations. (recommended)
-    - `'regression'`: Scores are the R2-scores of multivariable regression.
-    - `'regress_data'`: Scores are the R2-score of a sigmoidal fit.
-    - `'mi'`: Scores are the mutual information scores of the e-fields and the response variables.
-
-- ``scoring_emag_thr``: Threshold above which elements are scored. 
-More specifically: Per element, the `e_mag_max` as the
-maximum e-field magnitude reached in all zaps indicates how accessible an element is to stimulation (gyral element have
-the highest `e_mag_max`). This parameter is the lower bound for the `e_mag_max` of all scored elements. 
-  - Remark: The higher the threshold, the higher the scored elements are on the cortical ROI.
-
-- ``scoring_interval``: Interval at which elements are scored, determines subsampling resolution.
-  - Remark: `1/scoring_interval` elements are scored. Adjust to balance between computational efficiency and scoring detail.
-
-<u>Detection</u>
-
-- ``acc_thr``: Lower bound for the accuracy (clf) or scores (other scoring methods) of hotspot elements. Below that, 
-an element will not be categorized as hotspot.
-  - Remark: Remark: See recommendation sheet``data/network mapping configuration/recommendations_for_accuracy_threshold.md``.
-  For the clf-method, there is a table included recommending accuracy thresholds based on sample size.
-
-- ``corr_thr``: Correlation threshold (upper bound) for hotspot pairs. 
-  - Remark: When a second hotspot candidate too highly 
-  correlates with the first one, it is ignored, to avoid double detection of a single hotspot. Preliminary analyses have 
-  shown that this threshold does not have a lot of impact.
-  - 1: no limitation to how correlated they are, 0: only one hotspot allowed)
-
-- ``note``: Arbitrary string for additional comments or notes.
-
-The remaining 5 entries are not saved in the results overview. Namely the following: 
-
-<u>Evaluation</u>
-
-- ``save_files``: (boolean) Whether to save hotspot scores and scoremaps as HDF5 files.
-
-- ``fn_results``: Filename for the CSV the results/evaluation should be saved in.
-To understand output, see ``output_documentation``.
-
-<u>Plotting</u> 
-
-- ``plot_std``: (boolean) Whether to plot the response data with color indicating response value, and the e-field values
-of the chosen hotspots on x- and y-axis.
-
-- ``plot_bin``: (boolean) Whether to plot the binarized response data with color indicating response category, 
-and the e-field values of the chosen hotspots on x- and y-axis.
-
-- ``plot_curves``: (boolean) Whether to create two response data scatter plots, one for each chosen hotspot. (e-field 
-magnitudes on x-axis, response on y-axis).

pynibs/data/network mapping configuration/configuration_TEMPLATE.yaml

@@ -1,42 +0,0 @@
-# This configuration file contains settings and parameters for the application of the network detection algorithm.
-
-# BINARIZATION
-# binarization threshold is calculated as follows: method(response) * bin_factor
-bin_method: 'mean'           # mean, median or slope
-bin_factor: 1.0
-
-# SCORING
-scoring_method: 'clf'         # dual network expected: 'clf' or 'regression', single hotspot expected: 'regress_data' or 'mi'
-scoring_emag_thr: 0           # elements with `max(e_mag) > scoring_emag_thr` are scored
-scoring_interval: 22          # subsampling resolution: `1/scoring_interval' of all elements are scored
-
-# DETECTION
-acc_thr: 0.70                  # accuracy threshold for hotspot elements (lower bound)
-corr_thr: 0.5                 # correlation(hot0, hot1) threshold for hotspot pairs (upper bound)
-
-# ADDITIONAL INFO
-note: 'MI_score mapping reasons'     # arbitrary string    # NO COMMAS
-fn_flag: 'testrun_11'              # mentioned in the file name
-subject_id: '35357.53'          #'09440.22' # '13061.30' 35334.2b
-response_spec: 'FDI'            # specification (if any) to retrieve the response
-efield_spec: 'E_mag'            # E_mag, E_tan, E_norm
-
-
-####################################################
-# The following is not saved in the evaluation sheet:
-####################################################
-
-save_files: True                # whether to save experimental data & hotspot score data as hdf5
-write_effect_map: True          # whether to create effect map which can be used during validation
-fn_results: 'evaluation_template'             # file name of the .csv to save the results in
-
-# EFFECT
-# parameters used to create effect map - depends on e-field data and does not influence mapping result
-effect_full: 42             # at what e-field magnitude the desired effect is expected to manifest fully
-effect_saturation: 70       # at what e-mag the desired effect should saturate
-
-# PLOTTING of the found data (not in evaluation sheet)
-plot_std: True                # plot e-mag hotspot0 x emag hotspot1 x response
-plot_bin: True                # plot e-mag hotspot0 x emag hotspot1 x binarized response
-plot_curves: True             # plot e-mag hotspot0 x response and e-mag hotspot1 x response
-