[ENH] Make png default (#427)

* Makes --png default, adds --nopng

* Fixes integration test for --nopng

* Adds correction to integration test outputs

tedana/tests/data/tedana_outputs_verbose.txt

@@ -42,3 +42,80 @@ t2sv.nii.gz
 t2svG.nii.gz
 ts_OC.nii.gz
 ts_OC_whitened.nii.gz
+figures
+figures/Component_Overview.png
+figures/Kappa_vs_Rho_Scatter.png
+figures/comp_000.png
+figures/comp_001.png
+figures/comp_002.png
+figures/comp_003.png
+figures/comp_004.png
+figures/comp_005.png
+figures/comp_006.png
+figures/comp_007.png
+figures/comp_008.png
+figures/comp_009.png
+figures/comp_010.png
+figures/comp_011.png
+figures/comp_012.png
+figures/comp_013.png
+figures/comp_014.png
+figures/comp_015.png
+figures/comp_016.png
+figures/comp_017.png
+figures/comp_018.png
+figures/comp_019.png
+figures/comp_020.png
+figures/comp_021.png
+figures/comp_022.png
+figures/comp_023.png
+figures/comp_024.png
+figures/comp_025.png
+figures/comp_026.png
+figures/comp_027.png
+figures/comp_028.png
+figures/comp_029.png
+figures/comp_030.png
+figures/comp_031.png
+figures/comp_032.png
+figures/comp_033.png
+figures/comp_034.png
+figures/comp_035.png
+figures/comp_036.png
+figures/comp_037.png
+figures/comp_038.png
+figures/comp_039.png
+figures/comp_040.png
+figures/comp_041.png
+figures/comp_042.png
+figures/comp_043.png
+figures/comp_044.png
+figures/comp_045.png
+figures/comp_046.png
+figures/comp_047.png
+figures/comp_048.png
+figures/comp_049.png
+figures/comp_050.png
+figures/comp_051.png
+figures/comp_052.png
+figures/comp_053.png
+figures/comp_054.png
+figures/comp_055.png
+figures/comp_056.png
+figures/comp_057.png
+figures/comp_058.png
+figures/comp_059.png
+figures/comp_060.png
+figures/comp_061.png
+figures/comp_062.png
+figures/comp_063.png
+figures/comp_064.png
+figures/comp_065.png
+figures/comp_066.png
+figures/comp_067.png
+figures/comp_068.png
+figures/comp_069.png
+figures/comp_070.png
+figures/comp_071.png
+figures/comp_072.png
+figures/comp_073.png

tedana/tests/test_integration.py

@@ -112,7 +112,7 @@ def test_integration_three_echo(skip_integration):
         data='/tmp/data/three-echo/three_echo_Cornell_zcat.nii.gz',
         tes=[14.5, 38.5, 62.5],
         out_dir=out_dir,
-        tedpca='kundu', png=True)
+        tedpca='kundu')
 
     # compare the generated output files
     fn = resource_filename('tedana', 'tests/data/tedana_outputs.txt')

tedana/workflows/tedana.py

@@ -148,8 +148,8 @@ def _get_parser():
                                 'Set to -1 for varying results across ICA calls. '
                                 'Default=42.'),
                           default=42)
-    optional.add_argument('--png',
-                          dest='png',
+    optional.add_argument('--no-png',
+                          dest='no_png',
                           action='store_true',
                           help=('Creates a figures folder with static component '
                                 'maps, timecourse plots and other diagnostic '
@@ -213,7 +213,8 @@ def tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None,
                     tedort=False, gscontrol=None, tedpca='mle',
                     source_tes=-1, combmode='t2s', verbose=False, stabilize=False,
                     out_dir='.', fixed_seed=42, maxit=500, maxrestart=10,
-                    debug=False, quiet=False, png=False, png_cmap='coolwarm',
+                    debug=False, quiet=False, no_png=False,
+                    png_cmap='coolwarm',
                     low_mem=False, fittype='loglin'):
     """
     Run the "canonical" TE-Dependent ANAlysis workflow.
@@ -261,11 +262,11 @@ def tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None,
         which is slightly slower but may be more accurate.
     verbose : :obj:`bool`, optional
         Generate intermediate and additional files. Default is False.
-    png : obj:'bool', optional
-        Generate simple plots and figures. Default is false.
+    no_png : obj:'bool', optional
+        Do not generate .png plots and figures. Default is false.
     png_cmap : obj:'str', optional
             Name of a matplotlib colormap to be used when generating figures.
-            --png must still be used to request figures. Default is 'coolwarm'
+            Cannot be used with --no-png. Default 'coolwarm'
     out_dir : :obj:`str`, optional
         Output directory.
 
@@ -375,9 +376,13 @@ def tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None,
     n_samp, n_echos, n_vols = catd.shape
     LGR.debug('Resulting data shape: {}'.format(catd.shape))
 
+    if no_png and (png_cmap != 'coolwarm'):
+        LGR.warning('Overriding --no-png since --png-cmap provided.')
+        no_png = False
+
     # check if TR is 0
     img_t_r = ref_img.header.get_zooms()[-1]
-    if img_t_r == 0 and png:
+    if img_t_r == 0 and not no_png:
         raise IOError('Dataset has a TR of 0. This indicates incorrect'
                       ' header information. To correct this, we recommend'
                       ' using this snippet:'
@@ -537,7 +542,7 @@ def tedana_workflow(data, tes, mask=None, mixm=None, ctab=None, manacc=None,
     if verbose:
         io.writeresults_echoes(catd, mmix, mask, comptable, ref_img)
 
-    if png:
+    if not no_png:
         LGR.info('Making figures folder with static component maps and '
                  'timecourse plots.')
         # make figure folder first