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Paper revision changes so far
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@mathieuboudreau
mathieuboudreau committed Apr 12, 2024
1 parent cd1d012 commit 43e04e5
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Showing 3 changed files with 93 additions and 23 deletions.
2 changes: 2 additions & 0 deletions source/tools/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,6 +56,8 @@ class Data:
['qmri', 3, 10, 'T1w'],
['qmri', 4, 5, 'T1w'],
['qmri', 5, 7, 'T2w'],
['spine', 2, 10, 'GMT2w'],
['spine', 5, 5, 'GMT2w'],
['qmri', 2, 1, 'DWI_FA'], ['qmri', 2, 1, 'DWI_MD'], ['qmri', 2, 1, 'DWI_RD'],
['qmri', 3, 3, 'DWI_FA'], ['qmri', 3, 3, 'DWI_MD'], ['qmri', 3, 3, 'DWI_RD'],
['qmri', 6, 8, 'DWI_FA'], ['qmri', 6, 8, 'DWI_MD'], ['qmri', 6, 8, 'DWI_RD']
Expand Down
47 changes: 25 additions & 22 deletions source/tools/plot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ class Plot:
"""

colours = [(31, 119, 180), (174, 199, 232), (255, 127, 14), (190, 77, 80), (0, 132, 53),
colours = [(31, 119, 180), (174, 199, 232), (255, 127, 14), (190, 77, 80), (229, 153, 50), (0, 132, 53),
(255, 187, 120), (44, 160, 44), (152, 223, 138), (214, 39, 40), (255, 152, 150),
(148, 103, 189), (197, 176, 213), (140, 86, 75), (196, 156, 148),
(227, 119, 194), (247, 182, 210), (127, 127, 127), (199, 199, 199),
Expand Down Expand Up @@ -108,7 +108,7 @@ def display(self, env, fig_id = None):
init_notebook_mode(connected = True)
config={
'showLink': False,
'displayModeBar': False,
'displayModeBar': True,
'toImageButtonOptions': {
'format': 'png', # one of png, svg, jpeg, webp
'filename': 'custom_image',
Expand Down Expand Up @@ -266,7 +266,7 @@ def display(self, env, fig_id = None):
dict(label="MTR",
method="update",
args=[{"visible": [True] + [False]*(num_subjects*2) + [True]*num_subjects + [False]*num_subjects + [False]*2 + [True]*1 +[False]*1 + [False]*2 + [True]*1 +[False]*1 + [False]*(num_subjects*2) + [True]*num_subjects + [False]*num_subjects + [False]*2 + [True]*1 +[False]*1 + [False]*2 + [True]*1 +[False]*1},
self.set_trace_layout(matrix=matrix, metric='MTR', title='MTR [a.u.]', tissues=['WM', 'GM']) ]),
self.set_trace_layout(matrix=matrix, metric='MTR', title='MTR [%]', tissues=['WM', 'GM']) ]),
dict(label="MTsat",
method="update",
args=[{"visible": [True] + [False]*(num_subjects*3) + [True]*num_subjects + [False]*3 + [True]*1 + [False]*3 + [True]*1 + [False]*(num_subjects*3) + [True]*num_subjects + [False]*3 + [True]*1 + [False]*3 + [True]*1},
Expand All @@ -284,7 +284,7 @@ def display(self, env, fig_id = None):
dict(label="DWI_FA",
method="update",
args=[{"visible": [True] + [True]*num_subjects + [False]*(num_subjects*2) + [True]*1 + [False]*2 + [True]*1 + [False]*2 + [True]*num_subjects + [False]*(num_subjects*2) + [True]*1 + [False]*2 + [True]*1 + [False]*2},
self.set_trace_layout(matrix=matrix, metric='DWI_FA', title='DWI_FA [a.u.]', tissues=['CC_1', 'MCP'])]),
self.set_trace_layout(matrix=matrix, metric='DWI_FA', title='DWI_FA', tissues=['CC_1', 'MCP'])]),
dict(label="DWI_MD",
method="update",
args=[{"visible": [True] + [False]*num_subjects + [True]*num_subjects + [False]*(num_subjects) + [False]*1 + [True]*1 +[False]*1 + [False]*1 + [True]*1 +[False]*1 + [False]*num_subjects + [True]*num_subjects + [False]*(num_subjects) + [False]*1 + [True]*1 +[False]*1 + [False]*1 + [True]*1 +[False]*1},
Expand All @@ -306,7 +306,7 @@ def display(self, env, fig_id = None):
dict(label="DWI_FA",
method="update",
args=[{"visible": [True] + [True]*num_subjects + [False]*(num_subjects*2) + [True]*1 + [False]*2 + [True]*1 + [False]*2 + [True]*num_subjects + [False]*(num_subjects*2) + [True]*1 + [False]*2 + [True]*1 + [False]*2 + [True]*num_subjects + [False]*(num_subjects*2) + [True]*1 + [False]*2 + [True]*1 + [False]*2},
self.set_trace_layout(matrix=matrix, metric='DWI_FA', title='DWI_FA [a.u.]', tissues=['genu', 'body', 'splenium'])]),
self.set_trace_layout(matrix=matrix, metric='DWI_FA', title='DWI_FA', tissues=['genu', 'body', 'splenium'])]),
dict(label="DWI_MD",
method="update",
args=[{"visible": [True] + [False]*num_subjects + [True]*num_subjects + [False]*(num_subjects) + [False]*1 + [True]*1 +[False]*1 + [False]*1 + [True]*1 +[False]*1 + [False]*num_subjects + [True]*num_subjects + [False]*(num_subjects) + [False]*1 + [True]*1 +[False]*1 + [False]*1 + [True]*1 +[False]*1 + [False]*num_subjects + [True]*num_subjects + [False]*(num_subjects) + [False]*1 + [True]*1 +[False]*1 + [False]*1 + [True]*1 +[False]*1,
Expand Down Expand Up @@ -371,7 +371,7 @@ def display(self, env, fig_id = None):
dict(label="DWI_FA",
method="update",
args=[{"visible": [True] + [True]*num_subjects + [False]*(num_subjects*5) + [True]*1 + [False]*5 + [True]*1 + [False]*5},
self.set_trace_layout(matrix=matrix, metric='DWI_FA', title='DWI_FA [a.u.]')]),
self.set_trace_layout(matrix=matrix, metric='DWI_FA', title='DWI_FA')]),
dict(label="DWI_MD",
method="update",
args=[{"visible": [True] + [False]*num_subjects + [True]*num_subjects + [False]*(num_subjects*4) + [False]*1 + [True]*1 +[False]*4 + [False]*1 + [True]*1 +[False]*4},
Expand All @@ -383,7 +383,7 @@ def display(self, env, fig_id = None):
dict(label="MTR",
method="update",
args=[{"visible": [True] + [False]*(num_subjects*3) + [True]*num_subjects + [False]*(num_subjects*2) + [False]*3 + [True]*1 +[False]*2 + [False]*3 + [True]*1 +[False]*2},
self.set_trace_layout(matrix=matrix, metric='MTR', title='MTR [a.u.]')]),
self.set_trace_layout(matrix=matrix, metric='MTR', title='MTR [%]')]),
dict(label="MTsat",
method="update",
args=[{"visible": [True] + [False]*(num_subjects*4) + [True]*num_subjects + [False]*num_subjects + [False]*4 + [True]*1 +[False]*1 + [False]*4 + [True]*1 +[False]*1},
Expand Down Expand Up @@ -416,11 +416,11 @@ def display(self, env, fig_id = None):
x_button=1.4
elif self.dataset.data_type == 'brain-diffusion':
yaxis_range = [self.get_val(np.append(matrix['CC_1']['DWI_FA'], matrix['MCP']['DWI_FA'], axis=0), 'min'), self.get_val(np.append(matrix['CC_1']['DWI_FA'], matrix['MCP']['DWI_FA'], axis=0), 'max')]
yaxis_title = 'DWI_FA [a.u.]'
yaxis_title = 'DWI_FA'
x_button=1.3
elif self.dataset.data_type == 'brain-diffusion-cc':
yaxis_range = [self.get_val(np.append(matrix['genu']['DWI_FA'], matrix['splenium']['DWI_FA'], axis=0), 'min'), self.get_val(np.append(matrix['genu']['DWI_FA'], matrix['splenium']['DWI_FA'], axis=0), 'max')]
yaxis_title = 'DWI_FA [a.u.]'
yaxis_title = 'DWI_FA'
x_button=1.3
y_button=0.5
elif self.dataset.data_type == 'spine':
Expand All @@ -438,7 +438,7 @@ def display(self, env, fig_id = None):
yaxis_title = 'Area [mm<sup>2</sup>]'
else:
yaxis_range = [self.get_val(matrix['DWI_FA'], 'min'), self.get_val(matrix['DWI_FA'], 'max')]
yaxis_title = 'DWI_FA [a.u.]'
yaxis_title = 'DWI_FA'
x_button=1.28
width = 680
height = 540
Expand Down Expand Up @@ -504,7 +504,7 @@ def display_paper_fig2(self, env, fig_id = None):
init_notebook_mode(connected = True)
config={
'showLink': False,
'displayModeBar': False,
'displayModeBar': True,
'toImageButtonOptions': {
'format': 'png', # one of png, svg, jpeg, webp
'filename': 'custom_image',
Expand Down Expand Up @@ -624,7 +624,7 @@ def display_paper_fig2(self, env, fig_id = None):
fig.update_yaxes(
type="linear",
title={
'text':'MTR [a.u.]',
'text':'MTR [%]',
'standoff':0
},
showgrid=False,
Expand Down Expand Up @@ -850,7 +850,7 @@ def display_paper_fig3(self, env, fig_id = None):
init_notebook_mode(connected = True)
config={
'showLink': False,
'displayModeBar': False,
'displayModeBar': True,
'toImageButtonOptions': {
'format': 'png', # one of png, svg, jpeg, webp
'filename': 'custom_image',
Expand Down Expand Up @@ -915,7 +915,7 @@ def display_paper_fig3(self, env, fig_id = None):
fig.update_yaxes(
type="linear",
title={
'text':'DWI_FA [a.u.]',
'text':'DWI_FA',
'standoff':0
},
showgrid=False,
Expand Down Expand Up @@ -1197,7 +1197,7 @@ def display_paper_fig4(self, env, fig_id = None):
init_notebook_mode(connected = True)
config={
'showLink': False,
'displayModeBar': False,
'displayModeBar': True,
'toImageButtonOptions': {
'format': 'png', # one of png, svg, jpeg, webp
'filename': 'custom_image',
Expand Down Expand Up @@ -1261,7 +1261,8 @@ def display_paper_fig4(self, env, fig_id = None):
linewidth=2,
tickfont = dict(size=self.y_label_tick_font_size-5),
title_font = dict(size = self.general_font_size-5),
range = [self.get_val(matrix['T1w'], 'min'), self.get_val(matrix['T1w'], 'max')],
autorange=False,
range = [40, 100],
row=1, col=1
)

Expand Down Expand Up @@ -1292,7 +1293,8 @@ def display_paper_fig4(self, env, fig_id = None):
tickfont = dict(size=self.y_label_tick_font_size-5),
tickformat='s',
title_font = dict(size = self.general_font_size-5),
range = [self.get_val(matrix['T2w'], 'min'), self.get_val(matrix['T2w'], 'max')],
autorange=False,
range = [40, 100],
row=1, col=2
)
fig.update_xaxes(
Expand Down Expand Up @@ -1421,7 +1423,7 @@ def display_paper_fig5(self, env, fig_id = None):
init_notebook_mode(connected = True)
config={
'showLink': False,
'displayModeBar': False,
'displayModeBar': True,
'toImageButtonOptions': {
'format': 'png', # one of png, svg, jpeg, webp
'filename': 'custom_image',
Expand Down Expand Up @@ -1512,7 +1514,7 @@ def display_paper_fig5(self, env, fig_id = None):
fig.update_yaxes(
type="linear",
title={
'text':'MTR [a.u.]',
'text':'MTR [%]',
'standoff':0
},
showgrid=False,
Expand Down Expand Up @@ -1570,7 +1572,7 @@ def display_paper_fig5(self, env, fig_id = None):
fig.update_yaxes(
type="linear",
title={
'text':'DWI_FA [a.u.]',
'text':'DWI_FA',
'standoff':0
},
showgrid=False,
Expand Down Expand Up @@ -1996,7 +1998,6 @@ def add_points(self, figb, matrix, trace_name, num_sessions, tissue=None, fig_id
name= name_T1w,
marker_color=marker_color),
row=row_T1w, col=col_T1w)

marker_color="rgb"+str(Plot.colours[3])
marker_symbol=symbols[5]
if fig_id == 'spine-csa-wm' or fig_id == 'paper_fig4':
Expand Down Expand Up @@ -2304,7 +2305,7 @@ def add_std_area(self, figb, matrix, trace_name, line, tissue=None, fig_id=None,
if tissue == 'WM' or tissue == 'CC_1' or tissue=='genu':
fillcolor='rgba(31, 119, 180, 0.15)'
elif tissue == 'splenium':
fillcolor='rgba(0, 132, 53, 0.15)'
fillcolor='rgba(229, 153, 50 0.15)'
else:
fillcolor='rgba(190, 77, 80, 0.15)'

Expand Down Expand Up @@ -2501,6 +2502,8 @@ def set_trace_layout(self, matrix, metric, title, tissues=None):
yaxis_range = [self.get_val(np.append(pre_concat, matrix[tissues[2]][metric], axis=0), 'min'), self.get_val(np.append(pre_concat, matrix[tissues[2]][metric], axis=0), 'max')]
else:
yaxis_range = [self.get_val(matrix[metric], 'min'), self.get_val(matrix[metric], 'max')]
if metric=='T1w' or metric=='T2w':
yaxis_range = [40,100]
if metric=='DWI_MD' or metric=='DWI_RD':
return {"yaxis": dict(
range = yaxis_range,
Expand Down
67 changes: 66 additions & 1 deletion source/tools/stats.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,58 @@ def build_df(self, tissue = None):
else:
self.df = df

def build_stats_table(self):
def ICC(self, metric):

if 'WM' in self.database.keys() or 'CC_1' in self.database.keys() or 'genu' in self.database.keys():
df = self.df[metric]
else:
df = self.df[metric].to_list()

num_subjects = len(df)

ICC = np.zeros(6)

subjectVariance = np.zeros(6) # Array of variance within each subject
subjectMeans = np.zeros(6) # Array of mean within each subject

wsVariance = None # within-subject variance (i.e. mean of subjectVariance)
bsVariance = None # between-subject variance (i.e. variance of subjectMeans)

# wsVariance
for idx, subject in enumerate(df):
subject_data = np.array([x for x in subject if str(x) != 'nan'])

num_sessions = len(subject_data)
subjectMeans[idx] = np.mean(subject_data)

subjectVariance[idx] = np.divide(np.sum(np.square(subject_data-subjectMeans[idx])), (num_sessions-1))

wsVariance = np.mean(subjectVariance)

# wsVariance
grandMean = np.nanmean(df)

bsVariance = np.divide(np.sum(np.square(subjectMeans-grandMean)), (num_subjects-1))

# ICC (intraclass correlation coefficient)

ICC = np.divide(np.square(bsVariance), (np.square(bsVariance) + np.square(wsVariance)))

## COVs

# wsVariance
subjectCOVs = np.zeros(6)
for idx, subject in enumerate(subjectVariance):
subjectCOVs[idx] = np.sqrt(subjectVariance[idx])/subjectMeans[idx]

wsCOV = np.mean(subjectCOVs) * 100

#bsVariance
bsCOV = np.std(subjectMeans)/grandMean * 100

return ICC, wsCOV, bsCOV

def build_stats_table(self):
metrics = self.df.keys()
columns = []
col_vals = []
Expand All @@ -91,6 +142,9 @@ def build_stats_table(self):
'intrasubject COV mean [%]': col_vals,
'intrasubject COV std [%]': col_vals,
'intersubject mean COV [%]': col_vals,
'ICC': col_vals,
'wsCOV': col_vals,
'bsCOV': col_vals
}

self.stats_table = pd.DataFrame.from_dict(df_setup, orient='index', columns=columns)
Expand All @@ -103,10 +157,21 @@ def build_stats_table(self):

intrasub_mean = np.nanmean(self.df[metric], axis=1)
self.stats_table[self.database2table[metric]]['intersubject mean COV [%]'] = np.divide(np.std(intrasub_mean),np.mean(intrasub_mean)) * 100

ICC, wsCOV, bsCOV = self.ICC(metric)
self.stats_table[self.database2table[metric]]['ICC'] = ICC
self.stats_table[self.database2table[metric]]['wsCOV'] = wsCOV
self.stats_table[self.database2table[metric]]['bsCOV'] = bsCOV

else:
intrasub_cov = np.divide(np.nanstd(self.df[metric].tolist(), axis=1), np.nanmean(self.df[metric].tolist(), axis=1)) * 100
self.stats_table[self.database2table[metric]]['intrasubject COV mean [%]'] = np.mean(intrasub_cov)
self.stats_table[self.database2table[metric]]['intrasubject COV std [%]'] = np.std(intrasub_cov)

intrasub_mean = np.nanmean(self.df[metric].tolist(), axis=1)
self.stats_table[self.database2table[metric]]['intersubject mean COV [%]'] = np.divide(np.std(intrasub_mean),np.mean(intrasub_mean)) * 100

ICC, wsCOV, bsCOV = self.ICC(metric)
self.stats_table[self.database2table[metric]]['ICC'] = ICC
self.stats_table[self.database2table[metric]]['wsCOV'] = wsCOV
self.stats_table[self.database2table[metric]]['bsCOV'] = bsCOV

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