[REF] Modularize metric calculation

Makefile

@@ -23,6 +23,9 @@ three-echo:
 four-echo:
 	@py.test --log-cli-level=INFO --cov-append --cov-report term-missing --cov=tedana -k test_integration_four_echo tedana/tests/test_integration.py
 
+four-echo:
+	@py.test --cov-append --cov-report term-missing --cov=tedana -k test_integration_four_echo tedana/tests/test_integration.py
+
 five-echo:
 	@py.test --log-cli-level=INFO --cov-append --cov-report term-missing --cov=tedana -k test_integration_five_echo tedana/tests/test_integration.py
 

docs/api.rst

@@ -93,11 +93,10 @@ API
 
 .. autosummary::
    :toctree: generated/
-   :template: function.rst
-
-   tedana.metrics.dependence_metrics
-   tedana.metrics.kundu_metrics
+   :template: module.rst
 
+   tedana.metrics.collect
+   tedana.metrics.dependence
 
 .. _api_selection_ref:
 

docs/conf.py

@@ -142,8 +142,8 @@
 
 # https://github.com/rtfd/sphinx_rtd_theme/issues/117
 def setup(app):
-    app.add_stylesheet('theme_overrides.css')
-    app.add_javascript("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js")
+    app.add_css_file('theme_overrides.css')
+    app.add_js_file("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js")
 
 
 html_favicon = '_static/tedana_favicon.png'

docs/zenodo.js

@@ -0,0 +1,90 @@
+// Copied from
+// https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js
+var getContent = function(url, acceptType, callback) {
+    var xhr = new XMLHttpRequest();
+    xhr.open('GET', url, true);
+    if (acceptType == 'application/json') {
+    	xhr.responseType = 'json';
+    }
+    xhr.setRequestHeader('Accept', acceptType);
+    xhr.onload = function() {
+        var status = xhr.status;
+        if (status === 200) {
+            callback(null, xhr.response);
+        } else {
+            callback(status, xhr.response);
+        }
+    };
+    xhr.send();
+};
+
+String.prototype.endsWith = function(suffix) {
+    return this.indexOf(suffix, this.length - suffix.length) !== -1;
+};
+
+function getZenodoIDFromTag(conceptRecID, tagName, callback) {
+    getContent('https://zenodo.org/api/records/?q=conceptrecid:' + conceptRecID + '%20AND%20related.identifier:*github*' + tagName + '&all_versions&sort=-version', 
+               'application/json',
+                function(err, data) {
+                if (err !== null) {
+                    callback(err, null);
+                } else {
+                    if (data.length == 0) {
+                      callback('No records found for this tag and Zenodo ID', null);
+                    } else if (data.length > 1) {
+                      callback('Ambiguous numnber of records (more than one) found for this tag and Zenodo ID', null);
+                    } else {
+                      targetID = data[0].id
+                      callback(null, targetID);
+                    }
+                }
+    });
+}
+
+function getLatestIDFromconceptID(conceptRecID, callback) {
+    getContent('https://zenodo.org/api/records/' + conceptRecID, 
+               'application/json',
+                function(err, data) {
+                if (err !== null) {
+                    callback(err, null);
+                } else {
+                    targetID = data.id
+                    callback(null, targetID);
+                }
+    });
+}
+
+function getCitation(recordID, style, callback) {
+  style = typeof style !== 'undefined' ? style : 'vancouver-brackets-no-et-al';
+	getContent('https://www.zenodo.org/api/records/' + recordID + '?style=' + style, 'text/x-bibliography',
+     function(err, data) {
+        if (err !== null) {
+           callback(err, null);
+        } else {
+           callback(null, data);
+        }
+      });
+}
+
+function getDOI(recordID, callback) {
+	getContent('https://www.zenodo.org/api/records/' + recordID, 'application/json',
+     function(err, data) {
+        if (err !== null) {
+           callback(err, null);
+        } else {
+           var DOI = data.doi;
+           callback(null, DOI);
+        }
+      });
+}
+
+function getBIBTEX(recordID, callback) {
+	getContent('https://www.zenodo.org/api/records/' + recordID, 'text/x-bibtex',
+     function(err, data) {
+        if (err !== null) {
+           callback(err, null);
+        } else {
+           callback(null, data);
+        }
+      });
+}

setup.cfg

@@ -9,7 +9,7 @@ parentdir_prefix =
 [flake8]
 max-line-length = 99
 exclude=*build/
-ignore = E126,E402,W504
+ignore = E126,E402,W503,W504
 per-file-ignores =
     */__init__.py:F401
 

tedana/decay.py

@@ -2,8 +2,10 @@
 Functions to estimate S0 and T2* from multi-echo data.
 """
 import logging
-import scipy
 import numpy as np
+import scipy
+from scipy import stats
+
 from tedana import utils
 
 LGR = logging.getLogger(__name__)
@@ -376,6 +378,13 @@ def fit_decay(data, tes, mask, adaptive_mask, fittype, report=True):
     t2s_full = utils.unmask(t2s_full, mask)
     s0_full = utils.unmask(s0_full, mask)
 
+    # set a hard cap for the T2* map
+    # anything that is 10x higher than the 99.5 %ile will be reset to 99.5 %ile
+    cap_t2s = stats.scoreatpercentile(t2s_limited.flatten(), 99.5,
+                                      interpolation_method='lower')
+    LGR.debug('Setting cap on T2* map at {:.5f}'.format(cap_t2s * 10))
+    t2s_limited[t2s_limited > cap_t2s * 10] = cap_t2s
+
     return t2s_limited, s0_limited, t2s_full, s0_full
 
 

tedana/decomposition/pca.py

@@ -227,12 +227,16 @@ def tedpca(data_cat, data_oc, combmode, mask, adaptive_mask, t2sG,
         varex_norm = varex / varex.sum()
 
     # Compute Kappa and Rho for PCA comps
-    # Normalize each component's time series
-    vTmixN = stats.zscore(comp_ts, axis=0)
-    comptable, _, metric_metadata, _, _ = metrics.dependence_metrics(
-        data_cat, data_oc, comp_ts, adaptive_mask, tes, io_generator,
-        reindex=False, mmixN=vTmixN, algorithm=None,
-        label='PCA', verbose=verbose
+    required_metrics = [
+        'kappa', 'rho', 'countnoise', 'countsigFT2', 'countsigFS0',
+        'dice_FT2', 'dice_FS0', 'signal-noise_t',
+        'variance explained', 'normalized variance explained',
+        'd_table_score'
+    ]
+    comptable, _ = metrics.collect.generate_metrics(
+        data_cat, data_oc, comp_ts, adaptive_mask,
+        tes, io_generator, 'PCA',
+        metrics=required_metrics, sort_by=None
     )
 
     # varex_norm from PCA overrides varex_norm from dependence_metrics,
@@ -249,7 +253,6 @@ def tedpca(data_cat, data_oc, combmode, mask, adaptive_mask, t2sG,
     if algorithm == 'kundu':
         comptable, metric_metadata = kundu_tedpca(
             comptable,
-            metric_metadata,
             n_echos,
             kdaw,
             rdaw,
@@ -258,7 +261,6 @@ def tedpca(data_cat, data_oc, combmode, mask, adaptive_mask, t2sG,
     elif algorithm == 'kundu-stabilize':
         comptable, metric_metadata = kundu_tedpca(
             comptable,
-            metric_metadata,
             n_echos,
             kdaw,
             rdaw,
@@ -282,13 +284,7 @@ def tedpca(data_cat, data_oc, combmode, mask, adaptive_mask, t2sG,
     temp_comptable = comptable.set_index("Component", inplace=False)
     io_generator.save_file(temp_comptable, "PCA metrics tsv")
 
-    metric_metadata["Component"] = {
-        "LongName": "Component identifier",
-        "Description": (
-            "The unique identifier of each component. "
-            "This identifier matches column names in the mixing matrix TSV file."
-        ),
-    }
+    metric_metadata = metrics.collect.get_metadata(temp_comptable)
     io_generator.save_file(metric_metadata, "PCA metrics json")
 
     decomp_metadata = {

tedana/io.py

@@ -59,6 +59,8 @@ class OutputGenerator():
         This will correspond to a "figures" subfolder of ``out_dir``.
     prefix : str
         Prefix to prepend to output filenames.
+    verbose : bool
+        Whether or not to generate verbose output
     """
 
     def __init__(
@@ -68,7 +70,8 @@ def __init__(
         out_dir=".",
         prefix="",
         config="auto",
-        make_figures=True
+        make_figures=True,
+        verbose=False,
     ):
 
         if config == "auto":
@@ -94,6 +97,7 @@ def __init__(
         self.out_dir = op.abspath(out_dir)
         self.figures_dir = op.join(out_dir, "figures")
         self.prefix = prefix + "_" if prefix != "" else ""
+        self.verbose = verbose
 
         if not op.isdir(self.out_dir):
             LGR.info(f"Generating output directory: {self.out_dir}")

tedana/metrics/__init__.py

@@ -1,10 +1,7 @@
 # emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-
 # ex: set sts=4 ts=4 sw=4 et:
+"""TE-dependence and TE-independence metrics."""
 
-from .kundu_fit import (
-    dependence_metrics, kundu_metrics
-)
+from .collect import generate_metrics
 
-__all__ = [
-    'dependence_metrics', 'kundu_metrics'
-]
+__all__ = ["generate_metrics"]