Skip to content

Improved Defacing module (version 2?) #62

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 13 commits into
base: master
Choose a base branch
from
Open

Improved Defacing module (version 2?) #62

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
88c1abc
PEP
raamana Apr 7, 2022
89ec583
tweaking rating options
raamana Apr 7, 2022
4ffcd27
new param to allow user choice in slice lcoation
raamana Apr 7, 2022
b237f71
input validation
raamana Apr 7, 2022
062c194
implementing the input to display engine
raamana Apr 7, 2022
2e5e040
updated test
raamana Apr 7, 2022
fb6e60a
code quality / PEP
raamana Apr 7, 2022
ea46c97
tweaking options: adding Brows, but removing generic facial features
raamana Apr 8, 2022
158e69f
code quality
raamana Apr 21, 2022
2d72723
bug in keybd shortcut for fmri qc
raamana Jul 22, 2022
52f62fa
allowing use of pre-generated surf vis, regardless of whether FS is i…
raamana Jul 22, 2022
03d098d
getting started with native generation of 3d renders
raamana Mar 16, 2023
5b1227a
docs update
raamana Mar 16, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
113 changes: 63 additions & 50 deletions visualqc/config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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 = ''
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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

Expand All @@ -235,20 +238,22 @@
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',
e='othEr',
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

Expand All @@ -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

Expand All @@ -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]
## ----------------------------------------------------------------------------

Expand All @@ -331,23 +339,23 @@
# Registration and alignment specific
## ----------------------------------------------------------------------------

alignment_features_OLD = ('MSE', )
alignment_features_OLD = ('MSE',)
alignment_cmap = OrderedDict(Animate='gray',
Checkerboard='gray',
Voxelwise_diff='seismic',
Edges_Thinner=None,
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]
Expand All @@ -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

Expand All @@ -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
Expand All @@ -399,15 +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',
'r': 'eaRs visible',
'y': 'eYes visible',
'w': 'broWs 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)
Expand All @@ -424,3 +435,5 @@
'Mixed')

defacing_trim_percentile = 1

defacing_render_vis_angles = (-45, -22, 0, 22, 45)
Loading