From 88c1abc3c57c92063f0b9d546b2baa66058ff018 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Wed, 6 Apr 2022 20:31:59 -0400
Subject: [PATCH 01/13] PEP

---
 visualqc/config.py | 88 +++++++++++++++++++++++++---------------------
 1 file changed, 48 insertions(+), 40 deletions(-)

diff --git a/visualqc/config.py b/visualqc/config.py
index 82ee075..5967945 100644
--- a/visualqc/config.py
+++ b/visualqc/config.py
@@ -19,12 +19,14 @@
 statistic_in_histogram_freesurfer = 'ThickAvg'
 title_histogram_freesurfer = 'mean thickness (label-wise)'
 num_bins_histogram_display = 30
-xlim_histogram_freesurfer_all = { 'ThickAvg' : [1.0, 6.0], }
-xlim_histogram_freesurfer = xlim_histogram_freesurfer_all[statistic_in_histogram_freesurfer]
+xlim_histogram_freesurfer_all = {'ThickAvg': [1.0, 6.0], }
+xlim_histogram_freesurfer = xlim_histogram_freesurfer_all[
+    statistic_in_histogram_freesurfer]
 xticks_histogram_freesurfer = np.arange(1.5, 6.01, 1.0)
 color_histogram_freesurfer = ('#c9ae74')  # sandstone
 
-freesurfer_features_outlier_detection = ('cortical', 'subcortical', 'both', 'whole_brain')
+freesurfer_features_outlier_detection = ('cortical', 'subcortical',
+                                         'both', 'whole_brain')
 outlier_list_prefix = 'possible_outliers'
 alert_background_color = 'xkcd:coral'
 alert_colors_outlier = dict(cortical='xkcd:hot pink',
@@ -84,7 +86,7 @@
 mri_zorder_freesurfer = 0
 seg_zorder_freesurfer = 1
 
-background_value = 0 # for segmentations or MRI
+background_value = 0  # for segmentations or MRI
 
 default_views = (0, 1, 2)
 default_num_slices = 12
@@ -113,13 +115,14 @@
 #   there is a delay in processing the mouse events
 #   hence we increased delta t for double click from typical defaults of 0.5 sec to 1
 #   this also helps improving accessibility for those who cant click too fast
-double_click_time_delta = 1.1 # seconds
+double_click_time_delta = 1.1  # seconds
 
 # for serialization
 delimiter = ','
 # when ratings or notes contain the above delimiter, it will be replaced by this
 delimiter_replacement = ';'
-# when ratings are multiple (in some use cases), how to concat them into a single string without a delimiter
+# when ratings are multiple (in some use cases),
+#   how to concat them into a single string without a delimiter
 rating_joiner = '+'
 
 textbox_title = ''
@@ -154,8 +157,8 @@
                    bottom=0.06, top=0.98,
                    wspace=0.0, hspace=0.0)
 bounding_box_review = (review_area['left'], review_area['bottom'],
-                     review_area['right']-review_area['left'],
-                     review_area['top']-review_area['bottom'])
+                       review_area['right'] - review_area['left'],
+                       review_area['top'] - review_area['bottom'])
 no_blank_area = dict(left=0.01, right=0.99,
                      bottom=0.01, top=0.99,
                      wspace=0.05, hspace=0.02)
@@ -208,7 +211,7 @@
                              'Background only',
                              'Tails_trimmed',
                              'Original')
-saturate_perc_t1 = 33 # supra-threshold values are saturated.
+saturate_perc_t1 = 33  # supra-threshold values are saturated.
 num_bins_histogram_intensity_distribution = 100
 num_bins_histogram_contrast_enhancement = 256
 
@@ -243,12 +246,14 @@
                                                        t="i'm Tired",
                                                        v='reView later')
 func_mri_default_issue_list = list(abbreviation_func_mri_default_issue_list.values())
-func_mri_default_rating_list_shortform = abbreviation_func_mri_default_issue_list.keys()
+func_mri_default_rating_list_shortform = \
+    abbreviation_func_mri_default_issue_list.keys()
 
 func_outlier_features = None
 
 func_mri_BIDS_filters = dict(modalities='func')
-# usually done in analyses to try keep the numbers in numerical calculations away from small values
+# usually done in analyses to try keep the numbers in numerical calculations away
+# from small values
 # not important here, just for display, doing it anyways.
 scale_factor_BOLD = 1000
 
@@ -274,29 +279,32 @@
 
 diffusion_mri_pass_indicator = visual_qc_pass_indicator
 # f, s, l are matplotlib builtin shortcuts
-abbreviation_diffusion_mri_default_issue_list = OrderedDict(p=diffusion_mri_pass_indicator,
-                                                            m='Motion',
-                                                            d='Dropout',
-                                                            v='Vibration',
-                                                            r='Ringing',
-                                                            s='Spikes',
-                                                            f='driFt (scanner)',
-                                                            l='puLsation',
-                                                            g='Geometric',
-                                                            h='gHosting',
-                                                            o='Orient/FOV',
-                                                            i='Implausible',
-                                                            e='othEr',
-                                                            t="i'm Tired",
-                                                            w='revieW later')
+abbreviation_diffusion_mri_default_issue_list = OrderedDict(
+    p=diffusion_mri_pass_indicator,
+    m='Motion',
+    d='Dropout',
+    v='Vibration',
+    r='Ringing',
+    s='Spikes',
+    f='driFt (scanner)',
+    l='puLsation',
+    g='Geometric',
+    h='gHosting',
+    o='Orient/FOV',
+    i='Implausible',
+    e='othEr',
+    t="i'm Tired",
+    w='revieW later')
 diffusion_mri_default_issue_list = list(
     abbreviation_diffusion_mri_default_issue_list.values())
-diffusion_mri_default_rating_list_shortform = abbreviation_diffusion_mri_default_issue_list.keys()
+diffusion_mri_default_rating_list_shortform = \
+    abbreviation_diffusion_mri_default_issue_list.keys()
 
 diffusion_outlier_features = None
 
 diffusion_mri_BIDS_filters = dict(modalities='dwi', types='dwi')
-# usually done in analyses to try keep the numbers in numerical calculations away from small values
+# usually done in analyses to try keep the numbers in numerical calculations away
+# from small values
 # not important here, just for display, doing it anyways.
 scale_factor_diffusion = 1000
 
@@ -322,7 +330,7 @@
                                           'Align b=0 edges')
 fontsize_radio_button_align_method_diffusion = 8
 
-position_rating_checkbox_diffusion  = [0.899, 0.30, 0.095, 0.35]
+position_rating_checkbox_diffusion = [0.899, 0.30, 0.095, 0.35]
 position_alignment_method_diffusion = [0.899, 0.66, 0.095, 0.10]
 ## ----------------------------------------------------------------------------
 
@@ -331,7 +339,7 @@
 #           Registration and alignment specific
 ## ----------------------------------------------------------------------------
 
-alignment_features_OLD = ('MSE', )
+alignment_features_OLD = ('MSE',)
 alignment_cmap = OrderedDict(Animate='gray',
                              Checkerboard='gray',
                              Voxelwise_diff='seismic',
@@ -339,15 +347,15 @@
                              Edges_Diffused=None,
                              Color_mix=None)
 choices_alignment_comparison = alignment_cmap.keys()
-alignment_default_vis_type = 'Edges_Thinner' # 'Checkerboard' # 'Animate'
+alignment_default_vis_type = 'Edges_Thinner'  # 'Checkerboard' # 'Animate'
 
-default_checkerboard_size = None # 25
+default_checkerboard_size = None  # 25
 edge_threshold_alignment = 0.4
 default_color_mix_alphas = (1, 1)
 
 position_alignment_radio_button_method = [0.895, 0.45, 0.1, 0.19]
 position_alignment_radio_button_rating = [0.895, 0.25, 0.1, 0.25]
-position_text_input_alignment  = [0.900, 0.20, 0.09, 0.1]
+position_text_input_alignment = [0.900, 0.20, 0.09, 0.1]
 position_next_button_alignment = [0.905, 0.10, 0.07, 0.03]
 position_quit_button_alignment = [0.905, 0.03, 0.07, 0.03]
 position_toggle_animation = [0.925, 0.63, 0.07, 0.05]
@@ -356,16 +364,16 @@
 annotate_foreground_properties = dict(fontsize='medium', color='xkcd:pale orange')
 
 position_histogram_alignment = [0.905, 0.7, 0.09, 0.1]
-title_histogram_alignment  = 'voxel-wise diff'
+title_histogram_alignment = 'voxel-wise diff'
 num_bins_histogram_alignment = 20
 xticks_histogram_alignment = np.arange(0.1, 1.01, 0.2)
-color_histogram_alignment  = ('#c9ae74')  # sandstone
+color_histogram_alignment = ('#c9ae74')  # sandstone
 
 delay_in_animation = 0.5
 num_times_to_animate = 5
 
 # edge detection and filtering
-weak_edge_threshold = 60 # percentile: must be integer >1 and < 100
+weak_edge_threshold = 60  # percentile: must be integer >1 and < 100
 num_iter_weak_edge_removal = 10
 median_filter_size = 3
 
@@ -377,19 +385,19 @@
 ## ----------------------------------------------------------------------------
 
 
-alignment_features_groupwise = ('MSE', )
+alignment_features_groupwise = ('MSE',)
 alignment_cmap_groupwise = 'seismic'
 choices_alignment_comparison_groupwise = ('Std. dev map',
                                           'Animate through',
                                           'Animate with ref',
                                           'show outliers')
-alignment_groupwise_default_vis_type = 'Std. dev map' # 'Checkerboard' # 'Animate'
+alignment_groupwise_default_vis_type = 'Std. dev map'  # 'Checkerboard' # 'Animate'
 
 ## ----------------------------------------------------------------------------
 
 outlier_feature_folder_name = 'features_outlier_detection'
-features_outlier_detection = freesurfer_features_outlier_detection + t1_mri_features_OLD + func_mri_features_OLD
-
+features_outlier_detection = freesurfer_features_outlier_detection + \
+                             t1_mri_features_OLD + func_mri_features_OLD
 
 ## ----------------------------------------------------------------------------
 #          defacing MRI scan quality

From 89ec583d86fd81b5f49c6de73fd84393fa227f8d Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Wed, 6 Apr 2022 20:32:26 -0400
Subject: [PATCH 02/13] tweaking rating options

---
 visualqc/config.py   | 21 ++++++++++++---------
 visualqc/defacing.py |  4 ++--
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/visualqc/config.py b/visualqc/config.py
index 5967945..59531f9 100644
--- a/visualqc/config.py
+++ b/visualqc/config.py
@@ -407,15 +407,18 @@
 default_render_name = 'render.png'
 
 defacing_pass_indicator = visual_qc_pass_indicator
-abbreviation_defacing_default_issue_list = {'p': defacing_pass_indicator,
-                                          'f': 'Fail',
-                                          'o': 'Overstripped',
-                                          'u': 'Understripped',
-                                          'e': 'something Else',
-                                          't': "i'm Tired",
-                                          'l': 'review Later'}
-defacing_default_issue_list = list(abbreviation_defacing_default_issue_list.values())
-defacing_default_rating_list_shortform = abbreviation_defacing_default_issue_list.keys()
+abbrev_defacing_default_issue_list = {'p': defacing_pass_indicator,
+                                      'f': 'Fail',
+                                      'b': 'Brain removed',
+                                      'c': 'faCial features',
+                                      'y': 'eYes visible',
+                                      'r': 'eaRs visible',
+                                      'u': 'Unique mark(s)',
+                                      'e': 'something Else',
+                                      't': "i'm Tired",
+                                      'l': 'review Later'}
+defacing_default_issue_list = list(abbrev_defacing_default_issue_list.values())
+defacing_default_rating_list_shortform = abbrev_defacing_default_issue_list.keys()
 
 bbox_defacing_MRI_review = (0.02, 0.02, 0.88, 0.7)
 bbox_defacing_render_review = (0.02, 0.72, 0.88, 0.3)
diff --git a/visualqc/defacing.py b/visualqc/defacing.py
index 3f72927..7a489e7 100644
--- a/visualqc/defacing.py
+++ b/visualqc/defacing.py
@@ -277,8 +277,8 @@ def on_keyboard(self, key_in):
             # notice parentheses at the end
             self.map_key_to_callback[key_pressed]()
         else:
-            if key_pressed in cfg.abbreviation_defacing_default_issue_list:
-                checked_label = cfg.abbreviation_defacing_default_issue_list[
+            if key_pressed in cfg.abbrev_defacing_default_issue_list:
+                checked_label = cfg.abbrev_defacing_default_issue_list[
                     key_pressed]
                 self.checkbox.set_active(
                     cfg.defacing_default_issue_list.index(checked_label))

From 4ffcd27ac9da241e04a15b26b512a3a75519fc1a Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Wed, 6 Apr 2022 21:16:13 -0400
Subject: [PATCH 03/13] new param to allow user choice in slice lcoation

---
 visualqc/defacing.py | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/visualqc/defacing.py b/visualqc/defacing.py
index 7a489e7..acdddac 100644
--- a/visualqc/defacing.py
+++ b/visualqc/defacing.py
@@ -625,6 +625,14 @@ def get_parser():
     Default: a new folder called ``{}`` will be created inside the input folder
     \n""".format(cfg.default_out_dir_name))
 
+    help_text_slice_locations = textwrap.dedent("""
+    Specifies the locations to slice the MRI volumes at, in percentage of depth
+    from one end to the other i.e. 1 indicates the first non-zero slice in that
+    view (coronal, sagittal etc), 50 would be in the middle, and 100 would be the
+    other end.
+    Default: {}.
+    \n""".format(cfg.defacing_slice_locations))
+
     in_out = parser.add_argument_group('Input and output', ' ')
 
     in_out.add_argument("-u", "--user_dir", action="store", dest="user_dir",
@@ -650,6 +658,12 @@ def get_parser():
     in_out.add_argument("-i", "--id_list", action="store", dest="id_list",
                         default=None, required=False, help=help_text_id_list)
 
+    layout = parser.add_argument_group('Layout options', ' ')
+
+    layout.add_argument("-s", "--slice_locations", action="store", dest="slice_loc",
+                        default=cfg.defacing_slice_locations, required=False,
+                        nargs='+', help=help_text_slice_locations)
+
     return parser
 
 
@@ -671,15 +685,15 @@ def make_workflow_from_user_options():
 
     vis_type = 'defacing'
 
-    user_dir, id_list, images_for_id, defaced_name, mri_name, render_name \
-        = check_inputs_defacing(user_args.user_dir, user_args.defaced_name,
-                                user_args.mri_name, user_args.render_name,
-                                user_args.id_list)
+    user_dir, id_list, images_for_id, defaced_name, mri_name, render_name, \
+    slice_loc = check_inputs_defacing(
+        user_args.user_dir, user_args.defaced_name, user_args.mri_name,
+        user_args.render_name, user_args.id_list, user_args.slice_loc)
 
     out_dir = check_out_dir(user_args.out_dir, user_dir)
 
     wf = RatingWorkflowDefacing(id_list, images_for_id, user_dir, out_dir,
-                                defaced_name, mri_name, render_name,
+                                defaced_name, mri_name, render_name, slice_loc,
                                 cfg.defacing_default_issue_list, vis_type)
 
     return wf

From b237f7102738d3fa6652e7d94b4806077e9e5716 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Wed, 6 Apr 2022 21:16:54 -0400
Subject: [PATCH 04/13] input validation

---
 visualqc/utils.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/visualqc/utils.py b/visualqc/utils.py
index e9442c2..e3f465d 100644
--- a/visualqc/utils.py
+++ b/visualqc/utils.py
@@ -1020,6 +1020,17 @@ def check_labels(vis_type, label_set):
     return vis_type, label_set
 
 
+def check_slice_locations_percent(slice_loc):
+    """Checks they are numbers between 0 and 100 inclusive"""
+
+    slice_loc = [float(sl) for sl in slice_loc]
+    if any([sl < 1 or sl > 100 for sl in slice_loc]):
+        raise ValueError('One or more slice locations specified is invalid. '
+                         'They must be between 1 and 100.')
+
+    return slice_loc
+
+
 def check_views(views):
     """Checks which views were selected."""
 
@@ -1053,7 +1064,8 @@ def check_string_is_nonempty(string, string_type='string'):
     return string
 
 
-def check_inputs_defacing(in_dir, defaced_name, mri_name, render_name, id_list_in):
+def check_inputs_defacing(in_dir, defaced_name, mri_name, render_name, id_list_in,
+                          slice_loc):
     """Validates the integrity of the inputs"""
 
     in_dir = realpath(in_dir)
@@ -1064,6 +1076,8 @@ def check_inputs_defacing(in_dir, defaced_name, mri_name, render_name, id_list_i
     mri_name = check_string_is_nonempty(mri_name, 'original MRI scan')
     render_name = check_string_is_nonempty(render_name, '3D rendered image')
 
+    slice_loc = check_slice_locations_percent(slice_loc)
+
     if id_list_in is not None:
         if not pexists(id_list_in):
             raise IOError('Given ID list does not exist @ \n'
@@ -1129,7 +1143,7 @@ def check_inputs_defacing(in_dir, defaced_name, mri_name, render_name, id_list_i
     print('{} subjects are usable for review.'.format(len(id_list_out)))
 
     return in_dir, np.array(id_list_out), images_for_id, \
-           defaced_name, mri_name, render_name
+           defaced_name, mri_name, render_name, slice_loc
 
 
 def print_time_stamp():

From 062c19489ac35e7a5e8c1238c8aea2266cdddfde Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Wed, 6 Apr 2022 21:17:29 -0400
Subject: [PATCH 05/13] implementing the input to display engine

---
 visualqc/defacing.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/visualqc/defacing.py b/visualqc/defacing.py
index acdddac..bc80e0f 100644
--- a/visualqc/defacing.py
+++ b/visualqc/defacing.py
@@ -300,6 +300,7 @@ def __init__(self,
                  defaced_name,
                  mri_name,
                  render_name,
+                 slice_loc,
                  issue_list=cfg.defacing_default_issue_list,
                  vis_type='defacing'):
         """Constructor"""
@@ -315,13 +316,14 @@ def __init__(self,
         self.defaced_name = defaced_name
         self.mri_name = mri_name
         self.render_name = render_name
+        self.slice_loc = slice_loc
         self.images_for_id = images_for_id
 
         self.expt_id = 'rate_defaced_mri_{}'.format(self.defaced_name)
         self.suffix = self.expt_id
         self.current_alert_msg = None
 
-        self.init_layout()
+        self.init_layout(num_slices_per_view=len(self.slice_loc))
 
         self.__module_type__ = 'defacing'
 
@@ -458,7 +460,7 @@ def load_unit(self, unit_id):
         self.slice_picker = SlicePicker(self.orig_img,
                                         view_set=self.collage.view_set,
                                         num_slices=self.collage.num_slices,
-                                        sampler=cfg.defacing_slice_locations)
+                                        sampler=self.slice_loc)
 
         return skip_subject
 

From 2e5e040d50084ea4baeb6eb7610a1fdd10b180bc Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Wed, 6 Apr 2022 21:17:47 -0400
Subject: [PATCH 06/13] updated test

---
 visualqc/tests/test_defacing.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/visualqc/tests/test_defacing.py b/visualqc/tests/test_defacing.py
index 7fd8105..20995e5 100644
--- a/visualqc/tests/test_defacing.py
+++ b/visualqc/tests/test_defacing.py
@@ -9,14 +9,19 @@
 base_dir = realpath(pjoin(test_dir, '..', '..', 'example_datasets'))
 
 id_list = pjoin(base_dir, 'id_list_defacing')
-name_defaced = 'defaced_noniso2.nii.gz' # 'defaced.nii.gz'
-name_mri = 'orig_noniso2.nii.gz' # 'orig.nii.gz'
+name_defaced = 'defaced_noniso2.nii.gz'  # 'defaced.nii.gz'
+name_mri = 'orig_noniso2.nii.gz'  # 'orig.nii.gz'
 name_rendered = 'rendered.png'
 
+slice_locations = ' -s 40 45 47 50 55 57 60 '
+
 out_dir = pjoin(base_dir, 'out_defacing')
 makedirs(out_dir, exist_ok=True)
 
-sys.argv = shlex.split('visualqc_defacing -u {} -i {} -o {} -d {} -m {} -r {}'
+sys.argv = shlex.split('visualqc_defacing -u {} -i {} -o {} '
+                       '-d {} -m {} -r {} '
+                       ' {} '  # slice locations
                        ''.format(base_dir, id_list, out_dir,
-                                 name_defaced, name_mri, name_rendered))
+                                 name_defaced, name_mri, name_rendered,
+                                 slice_locations))
 cli_run()

From fb6e60a7b96a41fe422bfef3f6618c137b60ac68 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Thu, 7 Apr 2022 09:39:40 -0400
Subject: [PATCH 07/13] code quality / PEP

---
 visualqc/utils.py     | 9 ++++-----
 visualqc/workflows.py | 6 ++----
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/visualqc/utils.py b/visualqc/utils.py
index e3f465d..b5948b3 100644
--- a/visualqc/utils.py
+++ b/visualqc/utils.py
@@ -234,7 +234,7 @@ def pick_slices(img, view_set, num_slices):
         slices_in_dim = [sn for sn in slices_in_dim if
                          sn >= 0 or sn <= num_non_empty]
         # adding view and slice # at the same time.
-        slices.extend([(view, slice) for slice in slices_in_dim])
+        slices.extend([(view, slice_) for slice_ in slices_in_dim])
 
     return slices
 
@@ -421,7 +421,7 @@ def restore_previous_ratings(qcw):
     incomplete_list = list(qcw.id_list)
     prev_done = []  # empty list
 
-    ratings_file, backup_name_ratings = get_ratings_path_info(qcw)
+    ratings_file, _ = get_ratings_path_info(qcw)
 
     if pexists(ratings_file):
         ratings, notes = load_ratings_csv(ratings_file)
@@ -433,8 +433,7 @@ def restore_previous_ratings(qcw):
         notes = dict()
 
     if len(prev_done) > 0:
-        print('\nRatings for {}/{} subjects were restored.'.format(len(prev_done),
-                                                                   len(qcw.id_list)))
+        print(f'\nRestored {len(prev_done)}/{len(qcw.id_list)} previous ratings')
 
     if len(incomplete_list) < 1:
         print('No subjects to review/rate - exiting.')
@@ -503,7 +502,7 @@ def summarize_ratings(ratings_file, out_dir=None):
     import re
     clean = lambda lbl: re.sub(r'\W+', '_', lbl.lower())
 
-    rating_dict, notes = load_ratings_csv(ratings_file)
+    rating_dict, _ = load_ratings_csv(ratings_file)
 
     rating_list = list()
     uniq_labels = set()
diff --git a/visualqc/workflows.py b/visualqc/workflows.py
index d2f9db6..401827c 100644
--- a/visualqc/workflows.py
+++ b/visualqc/workflows.py
@@ -314,8 +314,7 @@ def quit(self, input_event_to_ignore=None):
             self.quit_now = True
         else:
             print('You have not rated the current subject! '
-                  'Please rate it before you can advance '
-                  'to next subject, or to quit..')
+                  'Rate it before you can quit.')
 
 
     def next(self, input_event_to_ignore=None):
@@ -326,8 +325,7 @@ def next(self, input_event_to_ignore=None):
             self.quit_now = False
         else:
             print('You have not rated the current subject! '
-                  'Please rate it before you can advance '
-                  'to next subject, or to quit..')
+                  'Rate it before you can advance to the next subject.')
 
 
     def prepare_to_advance(self):

From ea46c97a8402706c964288d9ffad08c30332bb3d Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Fri, 8 Apr 2022 11:24:57 -0400
Subject: [PATCH 08/13] tweaking options: adding Brows, but removing generic
 facial features

---
 visualqc/config.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/visualqc/config.py b/visualqc/config.py
index 59531f9..db224af 100644
--- a/visualqc/config.py
+++ b/visualqc/config.py
@@ -410,9 +410,9 @@
 abbrev_defacing_default_issue_list = {'p': defacing_pass_indicator,
                                       'f': 'Fail',
                                       'b': 'Brain removed',
-                                      'c': 'faCial features',
-                                      'y': 'eYes visible',
-                                      'r': 'eaRs visible',
+                                      'r': 'eaRs  visible',
+                                      'y': 'eYes  visible',
+                                      'w': 'broWs visible',
                                       'u': 'Unique mark(s)',
                                       'e': 'something Else',
                                       't': "i'm Tired",

From 158e69fb7b2ddcd276b086b43b0bde2dd32395ec Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Thu, 21 Apr 2022 13:22:16 -0400
Subject: [PATCH 09/13] code quality

---
 visualqc/defacing.py   |  2 +-
 visualqc/freesurfer.py | 63 +++++++++++++++++++++++++-----------------
 visualqc/workflows.py  |  5 ++--
 3 files changed, 42 insertions(+), 28 deletions(-)

diff --git a/visualqc/defacing.py b/visualqc/defacing.py
index bc80e0f..ddc50df 100644
--- a/visualqc/defacing.py
+++ b/visualqc/defacing.py
@@ -688,7 +688,7 @@ def make_workflow_from_user_options():
     vis_type = 'defacing'
 
     user_dir, id_list, images_for_id, defaced_name, mri_name, render_name, \
-    slice_loc = check_inputs_defacing(
+        slice_loc = check_inputs_defacing(
         user_args.user_dir, user_args.defaced_name, user_args.mri_name,
         user_args.render_name, user_args.id_list, user_args.slice_loc)
 
diff --git a/visualqc/freesurfer.py b/visualqc/freesurfer.py
index 01fa8fd..b5c729f 100644
--- a/visualqc/freesurfer.py
+++ b/visualqc/freesurfer.py
@@ -38,6 +38,7 @@
 
 next_click = time.monotonic()
 
+
 class FreesurferReviewInterface(BaseReviewInterface):
     """Custom interface for rating the quality of Freesurfer parcellation."""
 
@@ -525,16 +526,17 @@ def add_histogram_panel(self):
     def update_histogram(self):
         """Updates histogram with current image data"""
 
-        # to update thickness histogram, you need access to full FS output or aparc.stats
+        # to update thickness histogram, we need access to full FS output/aparc.stats
         try:
-            distribution_to_show = read_aparc_stats_wholebrain(self.in_dir, self.current_unit_id,
-                                                   subset=(cfg.statistic_in_histogram_freesurfer,))
+            distrib_to_show = read_aparc_stats_wholebrain(
+                self.in_dir, self.current_unit_id,
+                subset=(cfg.statistic_in_histogram_freesurfer,))
         except:
             # do nothing
             return
 
-        # number of vertices is too high - so presenting mean ROI thickness is smarter!
-        _, _, patches_hist = self.ax_hist.hist(distribution_to_show, density=True,
+        # number of vertices is too high so presenting mean ROI thickness is smarter!
+        _, _, patches_hist = self.ax_hist.hist(distrib_to_show, density=True,
                                                bins=cfg.num_bins_histogram_display)
         self.ax_hist.set_xlim(cfg.xlim_histogram_freesurfer)
         self.ax_hist.relim(visible_only=True)
@@ -560,8 +562,8 @@ def add_alerts(self):
         if flagged_as_outlier:
             alerts_list = self.by_sample.get(self.current_unit_id,
                                              None)  # None, if id not in dict
-            print('\n\tFlagged as a possible outlier by these measures:\n\t\t{}'.format(
-                '\t'.join(alerts_list)))
+            print('\n\tFlagged as a possible outlier by these measures:\n\t\t{}'
+                  ''.format('\t'.join(alerts_list)))
 
             strings_to_show = ['Flagged as an outlier:', ] + alerts_list
             self.current_alert_msg = '\n'.join(strings_to_show)
@@ -586,7 +588,8 @@ def load_unit(self, unit_id):
 
         skip_subject = False
         if self.vis_type in ('cortical_volumetric', 'cortical_contour'):
-            temp_seg_uncropped, roi_set_is_empty = void_subcortical_symmetrize_cortical(temp_fs_seg)
+            temp_seg_uncropped, roi_set_is_empty = \
+                void_subcortical_symmetrize_cortical(temp_fs_seg)
         elif self.vis_type in ('labels_volumetric', 'labels_contour'):
             if self.label_set is not None:
                 # TODO same colors for same labels is not guaranteed
@@ -595,7 +598,7 @@ def load_unit(self, unit_id):
                 temp_seg_uncropped, roi_set_is_empty = get_label_set(temp_fs_seg,
                                                                      self.label_set)
             else:
-                raise ValueError('--label_set must be specified for visualization types: '
+                raise ValueError('--label_set must be specified for vis types: '
                                  ' labels_volumetric and labels_contour')
         else:
             raise NotImplementedError('Invalid visualization type - '
@@ -848,7 +851,8 @@ def run_tksurfer_script(fs_dir, subject_id, hemi, script_file):
     try:
         cmd_args = ['tksurfer', '-sdir', fs_dir, subject_id, hemi, 'pial',
                     '-tcl', script_file]
-        txt_out = check_output(cmd_args, shell=False, stderr=subprocess.STDOUT, universal_newlines=True)
+        txt_out = check_output(cmd_args, shell=False, stderr=subprocess.STDOUT,
+                               universal_newlines=True)
     except subprocess.CalledProcessError as tksurfer_exc:
         exit_code = tksurfer_exc.returncode
         txt_out = tksurfer_exc.output
@@ -865,7 +869,8 @@ def run_freeview_script(script_file):
 
     try:
         cmd_args = ['freeview', '--command', script_file]
-        txt_out = check_output(cmd_args, shell=False, stderr=subprocess.STDOUT, universal_newlines=True)
+        txt_out = check_output(cmd_args, shell=False, stderr=subprocess.STDOUT,
+                               universal_newlines=True)
     except subprocess.CalledProcessError as tksurfer_exc:
         exit_code = tksurfer_exc.returncode
         txt_out = tksurfer_exc.output
@@ -886,7 +891,7 @@ def get_parser():
                                                  'of Freesurfer reconstruction.')
 
     help_text_fs_dir = textwrap.dedent("""
-    Absolute path to ``SUBJECTS_DIR`` containing the finished runs of Freesurfer parcellation
+    Absolute path to ``SUBJECTS_DIR`` containing the finished Freesurfer processing.
     Each subject will be queried after its ID in the metadata file.
 
     E.g. ``--fs_dir /project/freesurfer_v5.3``
@@ -934,24 +939,26 @@ def get_parser():
     \n""".format(cfg.default_vis_type))
 
     help_text_label = textwrap.dedent("""
-    Specifies the set of labels to include for overlay.
-
-    Atleast one label must be specified when vis_type is labels_volumetric or labels_contour
+    Specifies the set of labels to include for overlay. Atleast one label must be
+    specified when vis_type is labels_volumetric or labels_contour
 
     Default: None (show nothing)
     \n""")
 
     help_text_contour_color = textwrap.dedent("""
-    Specifies the color to use for the contours overlaid on MRI (when vis_type requested prescribes contours).
-    Color can be specified in many ways as documented in https://matplotlib.org/users/colors.html
+    Specifies the color to use for the contours overlaid on MRI, when vis_type
+      requested prescribes contours). Color can be specified in many ways
+      as documented in https://matplotlib.org/users/colors.html
     Default: {}.
     \n""".format(cfg.default_contour_face_color))
 
     help_text_alphas = textwrap.dedent("""
     Alpha values to control the transparency of MRI and aseg.
-    This must be a set of two values (between 0 and 1.0) separated by a space e.g. --alphas 0.7 0.5.
+    This must be a set of two values (between 0 and 1.0) separated by a space
+    e.g. --alphas 0.7 0.5.
 
-    Default: {} {}.  Play with these values to find something that works for you and the dataset.
+    Default: {} {}.
+    Play with these values to find something that works for you and the dataset.
     \n""".format(cfg.default_alpha_mri, cfg.default_alpha_seg))
 
     help_text_views = textwrap.dedent("""
@@ -972,9 +979,13 @@ def get_parser():
     \n""".format(cfg.default_num_rows))
 
     help_text_no_surface_vis = textwrap.dedent("""
-    This flag disables batch-generation of 3d surface visualizations, which are shown along with cross-sectional overlays. This is not recommended, but could be used in situations where you do not have Freesurfer installed or want to focus solely on cross-sectional views.
+    This flag disables batch-generation of 3d surface visualizations, which are shown
+    along with cross-sectional overlays. This is not recommended, but could be used
+    in situations where you do not have Freesurfer installed, or want to focus
+    solely on cross-sectional views.
 
-    Default: False (required visualizations are generated at the beginning, which can take 5-10 seconds for each subject).
+    Default: False (required visualizations are generated at the beginning,
+        which can take 5-10 seconds for each subject).
     \n""")
 
     help_text_outlier_detection_method = textwrap.dedent("""
@@ -1051,7 +1062,8 @@ def get_parser():
                           required=False, help=help_text_alphas)
 
     outliers = parser.add_argument_group('Outlier detection',
-                                         'options related to automatically detecting possible outliers')
+                                         'options related to automatically detecting '
+                                         'possible outliers')
     outliers.add_argument("-olm", "--outlier_method", action="store",
                           dest="outlier_method",
                           default=cfg.default_outlier_detection_method, required=False,
@@ -1084,9 +1096,10 @@ def get_parser():
                         default=cfg.default_num_rows, required=False,
                         help=help_text_num_rows)
 
-    wf_args = parser.add_argument_group('Workflow', 'Options related to workflow '
-                                                    'e.g. to pre-compute resource-intensive features, '
-                                                    'and pre-generate all the visualizations required')
+    wf_args = parser.add_argument_group(
+        'Workflow', 'Options related to workflow e.g. to pre-compute '
+                    'resource-intensive features, and pre-generate all the '
+                    'visualizations required')
 
     wf_args.add_argument("-ns", "--no_surface_vis", action="store_true",
                          dest="no_surface_vis", help=help_text_no_surface_vis)
diff --git a/visualqc/workflows.py b/visualqc/workflows.py
index 401827c..2d07b66 100644
--- a/visualqc/workflows.py
+++ b/visualqc/workflows.py
@@ -179,6 +179,7 @@ def _join_ratings(str_list):
         else:
             return str_list
 
+
     def save_time_spent(self):
         """Saves time spent on each unit"""
 
@@ -349,8 +350,8 @@ def print_rating(self, subject_id):
 
         if subject_id in self.ratings:
             # checking if "i'm tired" or 'review later' appear in ratings
-            do_not_save = any([ rt.lower() in cfg.ratings_not_to_be_recorded
-                  for rt in self.ratings[subject_id]])
+            do_not_save = any([rt.lower() in cfg.ratings_not_to_be_recorded
+                               for rt in self.ratings[subject_id]])
 
             # not saving ratings meant not to be saved!
             if do_not_save:

From 2d72723dd09915ca6a51bd8f41f3f994947cdce1 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Fri, 22 Jul 2022 18:21:15 -0400
Subject: [PATCH 10/13] bug in keybd shortcut for fmri qc

---
 visualqc/config.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/visualqc/config.py b/visualqc/config.py
index db224af..80509d2 100644
--- a/visualqc/config.py
+++ b/visualqc/config.py
@@ -238,7 +238,7 @@
 abbreviation_func_mri_default_issue_list = OrderedDict(p=func_mri_pass_indicator,
                                                        m='Motion',
                                                        r='Ringing',
-                                                       s='Spikes',
+                                                       k='spiKes',
                                                        g='Ghosting',
                                                        o='Orient/FOV',
                                                        w='Weird',

From 52f62fa6bdffa418059b67a373c6135dc1f78e93 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Fri, 22 Jul 2022 18:26:13 -0400
Subject: [PATCH 11/13] allowing use of pre-generated surf vis, regardless of
 whether FS is installed or not

---
 visualqc/freesurfer.py | 129 ++++++++++++++++++++++++-----------------
 visualqc/utils.py      |   3 +-
 2 files changed, 77 insertions(+), 55 deletions(-)

diff --git a/visualqc/freesurfer.py b/visualqc/freesurfer.py
index b5c729f..0a65070 100644
--- a/visualqc/freesurfer.py
+++ b/visualqc/freesurfer.py
@@ -346,9 +346,6 @@ def generate_surface_vis(self):
         print('\nAttempting to generate surface visualizations of parcellation ...')
         self._freesurfer_installed, self._fs_vis_tool = \
             freesurfer_vis_tool_installed()
-        if not self._freesurfer_installed:
-            print('Freesurfer does not seem to be installed '
-                  '- skipping surface visualizations.')
 
         self.surface_vis_paths = dict()
         for sid in self.id_list:
@@ -704,7 +701,7 @@ def cleanup(self):
         plt.close('all')
 
 
-def make_vis_pial_surface(fs_dir, subject_id, out_dir,
+def make_vis_pial_surface(fs_dir, subj_id, out_dir,
                           FREESURFER_INSTALLED,
                           annot_file='aparc.annot',
                           vis_tool=cfg.freesurfer_vis_cmd):
@@ -718,59 +715,86 @@ def make_vis_pial_surface(fs_dir, subject_id, out_dir,
     hemis_long = ('left', 'right')
     vis_list = dict()
 
-    print('Processing {}'.format(subject_id))
+    print('Processing {}'.format(subj_id))
     for hemi, hemi_l in zip(hemis, hemis_long):
 
-        # generating necessary scripts
         vis_list[hemi_l] = dict()
-        if vis_tool == "freeview":
-            script_file, vis_files = make_freeview_script_vis_annot(
-                fs_dir, subject_id, hemi, out_vis_dir, annot_file)
-        elif vis_tool == "tksurfer":
-            script_file, vis_files = make_tcl_script_vis_annot(
-                subject_id, hemi_l, out_vis_dir, annot_file)
-        else:
-            pass
-
-        # not running the scripts if required files dont exist
-        surf_path = fs_dir / subject_id / 'surf' / '{}.pial'.format(hemi)
-        annot_path = fs_dir / subject_id / 'label' / '{}.{}'.format(hemi, annot_file)
-        if not surf_path.exists():
-            print(f"surface for {subject_id} {hemi_l} doesn't exist @\n {surf_path}")
-            continue
-        if not annot_path.exists():
-            print(f"Annot for {subject_id} {hemi_l} doesn't exist @\n{annot_path}")
-            continue
-
-        try:
-            # run the script only if all the visualizations were not generated before
-            all_vis_exist = all([vp.exists() for vp in vis_files.values()])
-            if not all_vis_exist and FREESURFER_INSTALLED:
-                if vis_tool == "freeview":
-                    _, _ = run_freeview_script(script_file)
-                elif vis_tool == "tksurfer":
-                    _, _ = run_tksurfer_script(fs_dir, subject_id, hemi, script_file)
-                else:
-                    pass
-
-            vis_list[hemi_l].update(vis_files)
-        except:
-            traceback.print_exc()
-            print(f'unable to generate 3D surf vis for {hemi} hemi - skipping')
-
-    # flattening it for easier use later on
+        vis_list[hemi_l] = make_vis_paths(subj_id, hemi, out_vis_dir, vis_tool)
+        all_vis_exist = all([vp.exists() for vp in vis_list[hemi_l].values()])
+        if not all_vis_exist:
+            # generating necessary scripts
+            if vis_tool == "freeview":
+                script_file, vis_files = make_freeview_script_vis_annot(
+                    fs_dir, subj_id, hemi, out_vis_dir, annot_file)
+            elif vis_tool == "tksurfer":
+                script_file, vis_files = make_tcl_script_vis_annot(
+                    subj_id, hemi_l, out_vis_dir, annot_file)
+            else: # when freesurfer is not installed or not in path
+                vis_files = make_vis_paths(subj_id, hemi, out_vis_dir)
+
+            # not running the scripts if required files don't exist
+            surf_path = fs_dir / subj_id / 'surf' / f'{hemi}.pial'
+            annot_path = fs_dir / subj_id / 'label' / f'{hemi}.{annot_file}'
+
+            if surf_path.exists() and annot_path.exists():
+                try:
+                    # run script only if all vis were not generated before
+                    if FREESURFER_INSTALLED:
+                        if vis_tool == "freeview":
+                            _, _ = run_freeview_script(script_file)
+                        elif vis_tool == "tksurfer":
+                            _, _ = run_tksurfer_script(fs_dir, subj_id, hemi, script_file)
+                        else:
+                            pass
+
+                    vis_list[hemi_l].update(vis_files)
+                except:
+                    traceback.print_exc()
+                    print(f'unable to generate 3D surf vis for {hemi} hemi. '
+                          f'skipping')
+            else:
+                if not surf_path.exists():
+                    print(f"surface for {subj_id} {hemi_l} doesn't exist @"
+                          f"\n {surf_path}")
+                if not annot_path.exists():
+                    print(f"Annot for {subj_id} {hemi_l} doesn't exist @"
+                          f"\n{annot_path}")
+
+    # flattening / reordering it for easier use later on
     out_vis_list = dict()
     for hemi_l, view in cfg.view_pref_order[vis_tool]:
         try:
             if vis_list[hemi_l][view].exists():
                 out_vis_list[(hemi_l, view)] = vis_list[hemi_l][view]
+            else:
+                print(f'no surf vis for {subj_id} {hemi_l} {view}')
         except:
-            # not file hemi/view combinations have files generated
+            # not all hemi/view combinations have vis files generated
             pass
 
     return out_vis_list
 
 
+def make_vis_paths(subject_id, hemi, out_vis_dir, vis_tool='freeview'):
+    """util to make output paths to store visualizations"""
+
+    vis_path = dict()
+    vis_tool = vis_tool.lower()
+    if vis_tool == 'freeview':
+        img_ext = 'png'
+        angles = cfg.freeview_surface_vis_angles
+    elif vis_tool == 'tksurfer':
+        img_ext = 'tif'
+        angles = cfg.tksurfer_surface_vis_angles
+    else:
+        raise ValueError('Invalid vis_tool, it must be freeview or tksurfer')
+
+    for view in angles:
+        vis_path[view] = out_vis_dir / f'{subject_id}_{hemi}_{view}.{img_ext}'
+
+    return vis_path
+
+
 def make_freeview_script_vis_annot(fs_dir, subject_id, hemi, out_vis_dir,
                                    annot_file='aparc.annot'):
     """Generates a tksurfer script to make visualizations"""
@@ -778,13 +802,12 @@ def make_freeview_script_vis_annot(fs_dir, subject_id, hemi, out_vis_dir,
     fs_dir = Path(fs_dir).resolve()
     out_vis_dir = Path(out_vis_dir).resolve()
 
+    vis_path = make_vis_paths(subject_id, hemi, out_vis_dir, vis_tool='freeview')
+
     surf_path = fs_dir / subject_id / 'surf' / '{}.pial'.format(hemi)
     annot_path = fs_dir / subject_id / 'label' / '{}.{}'.format(hemi, annot_file)
 
     script_file = out_vis_dir / 'vis_annot_{}.freeview.cmd'.format(hemi)
-    vis_path = dict()
-    for view in cfg.freeview_surface_vis_angles:
-        vis_path[view] = out_vis_dir / '{}_{}_{}.png'.format(subject_id, hemi, view)
 
     # NOTES reg freeview commands
     # --screenshot <FILENAME> <MAGIFICATION_FACTOR> <AUTO_TRIM>
@@ -814,10 +837,7 @@ def make_freeview_script_vis_annot(fs_dir, subject_id, hemi, out_vis_dir,
 def make_tcl_script_vis_annot(subject_id, hemi, out_vis_dir, annot_file='aparc.annot'):
     """Generates a tksurfer script to make visualizations"""
 
-    script_file = out_vis_dir / f'vis_annot_{hemi}.tcl'
-    vis = dict()
-    for view in cfg.tksurfer_surface_vis_angles:
-        vis[view] = out_vis_dir / f'{subject_id}_{hemi}_{view}.tif'
+    vis_path = make_vis_paths(subject_id, hemi, out_vis_dir, vis_tool='tksurfer')
 
     img_format = 'tiff'  # rgb does not work
 
@@ -826,23 +846,24 @@ def make_tcl_script_vis_annot(subject_id, hemi, out_vis_dir, annot_file='aparc.a
     cmds.append("labl_import_annotation {}".format(annot_file))
     cmds.append("scale_brain 1.37")
     cmds.append("redraw")
-    cmds.append("save_{} {}".format(img_format, vis['lateral']))
+    cmds.append("save_{} {}".format(img_format, vis_path['lateral']))
     cmds.append("rotate_brain_y 180.0")
     cmds.append("redraw")
-    cmds.append("save_{} {}".format(img_format, vis['medial']))
+    cmds.append("save_{} {}".format(img_format, vis_path['medial']))
     cmds.append("rotate_brain_z -90.0")
     cmds.append("rotate_brain_y 135.0")
     cmds.append("redraw")
-    cmds.append("save_{} {}".format(img_format, vis['transverse']))
+    cmds.append("save_{} {}".format(img_format, vis_path['transverse']))
     cmds.append("exit 0")
 
+    script_file = out_vis_dir / f'vis_annot_{hemi}.tcl'
     try:
         with open(script_file, 'w') as sf:
             sf.write('\n'.join(cmds))
     except:
         raise IOError('Unable to write the script file to\n {}'.format(script_file))
 
-    return script_file, vis
+    return script_file, vis_path
 
 
 def run_tksurfer_script(fs_dir, subject_id, hemi, script_file):
diff --git a/visualqc/utils.py b/visualqc/utils.py
index b5948b3..b839733 100644
--- a/visualqc/utils.py
+++ b/visualqc/utils.py
@@ -699,7 +699,8 @@ def freesurfer_vis_tool_installed():
 
     if os.getenv('FREESURFER_HOME') is None:
         print('the environment variable FREESURFER_HOME is not set!')
-        return False, None
+        # using freeview here instead of None to recognize existing visualizations
+        return False, "freeview"
 
     fv_callable = which('freeview') is not None
     if fv_callable:

From 03d098d59c5e2ec71afd1e31a74c1803589209d2 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Thu, 16 Mar 2023 12:09:13 -0400
Subject: [PATCH 12/13] getting started with native generation of 3d renders

---
 visualqc/config.py   |  2 ++
 visualqc/defacing.py | 77 +++++++++++++++++++++++++++++++++++++++++---
 visualqc/utils.py    | 10 ++++++
 3 files changed, 85 insertions(+), 4 deletions(-)

diff --git a/visualqc/config.py b/visualqc/config.py
index 80509d2..cadfcfa 100644
--- a/visualqc/config.py
+++ b/visualqc/config.py
@@ -435,3 +435,5 @@
                         'Mixed')
 
 defacing_trim_percentile = 1
+
+defacing_render_vis_angles = (-45, -22, 0, 22, 45)
diff --git a/visualqc/defacing.py b/visualqc/defacing.py
index ddc50df..9d58713 100644
--- a/visualqc/defacing.py
+++ b/visualqc/defacing.py
@@ -22,7 +22,7 @@
 from visualqc.utils import (check_event_in_axes, check_inputs_defacing,
                             check_out_dir, compute_cell_extents_grid,
                             pixdim_nifti_header, read_image, set_fig_window_title,
-                            slice_aspect_ratio)
+                            slice_aspect_ratio, rendering_tool_installed)
 from visualqc.workflows import BaseWorkflowVisualQC
 
 
@@ -302,6 +302,7 @@ def __init__(self,
                  render_name,
                  slice_loc,
                  issue_list=cfg.defacing_default_issue_list,
+                 disable_3d_renderings=False,
                  vis_type='defacing'):
         """Constructor"""
 
@@ -311,7 +312,6 @@ def __init__(self,
                          outlier_feat_types=None,
                          disable_outlier_detection=None)
 
-        self.vis_type = vis_type
         self.issue_list = issue_list
         self.defaced_name = defaced_name
         self.mri_name = mri_name
@@ -323,6 +323,9 @@ def __init__(self,
         self.suffix = self.expt_id
         self.current_alert_msg = None
 
+        self.vis_type = vis_type
+        self.disable_3d_renderings = disable_3d_renderings
+
         self.init_layout(num_slices_per_view=len(self.slice_loc))
 
         self.__module_type__ = 'defacing'
@@ -331,7 +334,8 @@ def __init__(self,
     def preprocess(self):
         """Preprocessing if necessary."""
 
-        pass
+        if not self.disable_3d_renderings:
+            self.generate_3d_renderings()
 
 
     def init_layout(self,
@@ -364,6 +368,20 @@ def init_layout(self,
         self.padding = padding
 
 
+    def generate_3d_renderings(self):
+        """batch generation of 3D renderings of the MRI volumes prior to review"""
+
+        print('\nAttempting to generate surface visualizations of parcellation ...')
+        self._rendering_tool_installed, self._rendering_tool = \
+            rendering_tool_installed()
+
+        self.render_vis_paths = dict()
+        for sid in self.id_list:
+            self.render_vis_paths[sid] = \
+                make_3d_render(self.images_for_id[sid]['original'], self.out_dir,
+                               self._rendering_tool_installed, self._rendering_tool)
+
+
     def prepare_UI(self):
         """Main method to run the entire workflow"""
 
@@ -571,6 +589,16 @@ def cleanup(self):
         plt.close('all')
 
 
+def make_3d_render(mri_path, out_dir, too_exists_flag, tool_path):
+    """generates 3D render of an MRI volume in different angles"""
+
+    vis_paths = list()  # list of paths to renderings at different angles
+
+    # fsleyes render --scene 3d -rot 45 0 -30 -dr 30 250 -cr 30 500
+    #   -in spline -bf 0.225 -r 100 -ns 500 --outfile img_render.png orig.nii.gz
+    return vis_paths
+
+
 def get_parser():
     """Parser to specify arguments and their defaults."""
 
@@ -635,6 +663,17 @@ def get_parser():
     Default: {}.
     \n""".format(cfg.defacing_slice_locations))
 
+    help_text_no_3d_renderings = textwrap.dedent("""
+    This flag disables batch-generation of 3d rendering of the MRI volume, which are
+    shown along with cross-sectional overlays. This is not recommended, but could
+    be used in situations where you can not generate them, or want to
+    focus solely on cross-sectional views.
+
+    Default: False (required visualizations are generated at the beginning,
+    if they don't exist already, which can take 5-10 seconds for each subject).
+    \n""")
+
+
     in_out = parser.add_argument_group('Input and output', ' ')
 
     in_out.add_argument("-u", "--user_dir", action="store", dest="user_dir",
@@ -666,9 +705,38 @@ def get_parser():
                         default=cfg.defacing_slice_locations, required=False,
                         nargs='+', help=help_text_slice_locations)
 
+    wf_args = parser.add_argument_group(
+        'Workflow', 'Options related to workflow e.g. to pre-compute '
+                    'resource-intensive features, and pre-generate all the '
+                    'visualizations required')
+
+    wf_args.add_argument("-nr", "--no_3d_renderings", dest="disable_3d_renderings",
+                         action="store_true", default=False,
+                         help=help_text_no_3d_renderings)
+
     return parser
 
 
+def make_vis_paths(subject_id, out_vis_dir, vis_tool='fsleyes'):
+    """util to make output paths to store visualizations"""
+
+    vis_path = dict()
+    vis_tool = vis_tool.lower()
+    if vis_tool == 'fsleyes':
+        img_ext = 'png'
+        angles = cfg.freeview_surface_vis_angles
+    elif vis_tool == 'tksurfer':
+        img_ext = 'tif'
+        angles = cfg.tksurfer_surface_vis_angles
+    else:
+        raise ValueError('Invalid vis_tool, it must be freeview or tksurfer')
+
+    for view in angles:
+        vis_path[view] = out_vis_dir / f'{subject_id}_{hemi}_{view}.{img_ext}'
+
+    return vis_path
+
+
 def make_workflow_from_user_options():
     """Parser/validator for the cmd line args."""
 
@@ -696,7 +764,8 @@ def make_workflow_from_user_options():
 
     wf = RatingWorkflowDefacing(id_list, images_for_id, user_dir, out_dir,
                                 defaced_name, mri_name, render_name, slice_loc,
-                                cfg.defacing_default_issue_list, vis_type)
+                                cfg.defacing_default_issue_list,
+                                user_args.disable_3d_renderings, vis_type)
 
     return wf
 
diff --git a/visualqc/utils.py b/visualqc/utils.py
index b839733..9118b28 100644
--- a/visualqc/utils.py
+++ b/visualqc/utils.py
@@ -718,6 +718,16 @@ def freesurfer_vis_tool_installed():
     return False
 
 
+def rendering_tool_installed():
+    """checks if the tool to generate 3D renderings of MRI volumes is installed"""
+
+    fe_callable = which('fsleyes') is not None
+    if fe_callable:
+        return True, "fsleyes"
+    else:
+        return False, None
+
+
 def check_out_dir(out_dir, base_dir):
     """Creates the output folder."""
 

From 5b1227a7fbd3bf4ad3976f64b60fd5d6d8503632 Mon Sep 17 00:00:00 2001
From: Pradeep Reddy Raamana <raamana@gmail.com>
Date: Thu, 16 Mar 2023 12:09:29 -0400
Subject: [PATCH 13/13] docs update

---
 visualqc/freesurfer.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/visualqc/freesurfer.py b/visualqc/freesurfer.py
index 0a65070..4f0a4e4 100644
--- a/visualqc/freesurfer.py
+++ b/visualqc/freesurfer.py
@@ -1006,7 +1006,7 @@ def get_parser():
     solely on cross-sectional views.
 
     Default: False (required visualizations are generated at the beginning,
-        which can take 5-10 seconds for each subject).
+    if they don't exist already, which can take 5-10 seconds for each subject).
     \n""")
 
     help_text_outlier_detection_method = textwrap.dedent("""
@@ -1122,8 +1122,9 @@ def get_parser():
                     'resource-intensive features, and pre-generate all the '
                     'visualizations required')
 
-    wf_args.add_argument("-ns", "--no_surface_vis", action="store_true",
-                         dest="no_surface_vis", help=help_text_no_surface_vis)
+    wf_args.add_argument("-ns", "--no_surface_vis", dest="no_surface_vis",
+                         action="store_true", default=False,
+                         help=help_text_no_surface_vis)
 
     return parser