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Jan Zelenka
prasopes
Commits
bd500ff9
Commit
bd500ff9
authored
Feb 22, 2021
by
Yan
Browse files
Reactivitytools - fix
* still many things broken
parent
f2adb015
Changes
4
Hide whitespace changes
Inline
Side-by-side
prasopes/__main__.py
View file @
bd500ff9
...
...
@@ -210,7 +210,7 @@ def paint_override(self, augCanvas):
self
.
plot
.
set_ylim
(
augCanvas
.
spectplot
.
get_ylim
())
data
=
[
line
.
get_data
()
for
line
in
augCanvas
.
spectplot
.
lines
]
texts
=
copy
.
copy
(
augCanvas
.
ms
)
if
augCanvas
.
ds
and
augCanvas
.
ds
.
headers
!=
[]
:
if
augCanvas
.
ds
and
augCanvas
.
ds
.
headers
:
legend
=
augCanvas
.
spectplot
.
get_legend
().
get_texts
()
[
gt
.
pop_plot
(
*
line
,
self
.
plot
,
texts
,
i
,
legend
[
i
].
get_text
(),
not
(
cf
.
settings
().
value
(
...
...
prasopes/datasets.py
View file @
bd500ff9
...
...
@@ -22,8 +22,8 @@ class Dataset():
self
.
filename
=
rawfile
self
.
chromatograms
=
[]
self
.
dataset
=
[]
self
.
headers
=
[]
self
.
params
=
[]
self
.
headers
=
None
self
.
params
=
None
self
.
mintime
=
-
np
.
inf
self
.
maxtime
=
np
.
inf
...
...
prasopes/graphtools.py
View file @
bd500ff9
...
...
@@ -28,8 +28,7 @@ class AugFigureCanvas(FigureCanvas):
super
().
__init__
(
self
.
figure
)
self
.
ds
=
None
self
.
ms
=
dict
(
annotation
=
[],
name
=
"Spectrum"
,
xlabel
=
"m/z"
,
ylabel
=
"ion count"
,
xtics
=
20
,
predict
=
None
,
params
=
[],
headers
=
[],
texts
=
[])
ylabel
=
"ion count"
,
xtics
=
20
,
predict
=
None
,
texts
=
[])
self
.
chrom
=
dict
(
x
=
[
0
],
y
=
[
0
],
t_start
=
None
,
t_end
=
None
,
machtype
=
None
,
name
=
"Chromatogram"
,
xlabel
=
"time(min)"
,
ylabel
=
"total ion count"
,
...
...
@@ -250,7 +249,7 @@ def plot_subtime(augCanvas):
augCanvas
.
spectplot
.
set_xlim
(
slims
[
0
])
if
not
cf
.
settings
().
value
(
"view/autozoomy"
,
type
=
bool
):
augCanvas
.
spectplot
.
set_ylim
(
slims
[
1
])
if
not
augCanvas
.
ds
.
headers
==
[]
:
if
augCanvas
.
ds
.
headers
:
for
ax
in
(
augCanvas
.
spectplot
,
augCanvas
.
chromplot
):
ax
.
legend
(
loc
=
2
)
ax
.
get_legend
().
set_in_layout
(
False
)
...
...
@@ -451,7 +450,8 @@ def populate(augCanvas):
chromxy
=
augCanvas
.
ds
.
chromatograms
msxy
=
augCanvas
.
ds
.
get_spectra
()
for
i
in
range
(
len
(
msxy
)):
if
len
(
augCanvas
.
ds
.
headers
)
==
len
(
augCanvas
.
ds
.
chromatograms
):
if
augCanvas
.
ds
.
headers
and
\
len
(
augCanvas
.
ds
.
headers
)
==
len
(
augCanvas
.
ds
.
chromatograms
):
legend
=
legendize
(
augCanvas
.
ds
.
headers
[
i
],
augCanvas
)
else
:
legend
=
None
...
...
@@ -459,7 +459,7 @@ def populate(augCanvas):
pop_plot
(
chromxy
[
i
][
0
],
chromxy
[
i
][
1
],
augCanvas
.
chromplot
,
augCanvas
.
chrom
,
i
,
legend
)
for
ax
in
(
augCanvas
.
spectplot
,
augCanvas
.
chromplot
):
if
not
augCanvas
.
ds
.
headers
==
[]
:
if
augCanvas
.
ds
.
headers
:
ax
.
legend
(
loc
=
2
)
ax
.
get_legend
().
set_in_layout
(
False
)
ax
.
get_legend
().
set_visible
(
...
...
@@ -471,7 +471,7 @@ def populate(augCanvas):
def
update_paramstable
(
augCanvas
):
if
augCanvas
.
ds
.
params
==
[]
:
if
not
augCanvas
.
ds
.
params
:
augCanvas
.
paramstable
.
setRowCount
(
0
)
return
elif
len
(
augCanvas
.
ds
.
params
[
0
])
==
augCanvas
.
paramstable
.
rowCount
():
...
...
prasopes/reactivitytools.py
View file @
bd500ff9
...
...
@@ -86,7 +86,7 @@ def key_pressed(event, augCanvas, drls, grph, labels, parselect):
def
export_dial
(
augCanvas
,
drls
,
grph
,
labels
,
parselect
):
"""exports the reactivity into the .dat file format"""
if
not
augCanvas
.
ds
:
if
not
augCanvas
.
ds
or
not
augCanvas
.
ds
.
params
:
QtWidgets
.
QMessageBox
.
warning
(
None
,
"Export spectrum"
,
"Nothing to export, cancelling request"
)
...
...
@@ -105,13 +105,13 @@ def export_dial(augCanvas, drls, grph, labels, parselect):
def
update_parselect
(
augCanvas
,
parselect
):
# Do not do anything when data set is not populated
if
not
augCanvas
.
ds
:
if
not
augCanvas
.
ds
or
not
augCanvas
.
ds
.
params
:
return
index
=
parselect
.
currentIndex
()
if
index
==
-
1
:
index
=
settings
.
value
(
"reactivity/index"
,
type
=
int
)
parlist
=
[
": "
.
join
([
str
(
i
),
j
])
for
i
,
j
in
enumerate
(
augCanvas
.
ms
[
'
params
'
]
[
0
])]
enumerate
(
augCanvas
.
ds
.
params
[
0
])]
parselect
.
clear
()
parselect
.
addItems
(
parlist
)
if
index
<=
len
(
parlist
):
...
...
@@ -126,7 +126,7 @@ def tab_changed(fnc, index):
def
pop_dial
(
augCanvas
,
drls
,
graph
,
labels
,
parselect
):
logger
.
debug
(
"populating reactivity dialog"
)
# Do not do anything when data set is not populated
if
not
augCanvas
.
ds
:
if
not
augCanvas
.
ds
or
not
augCanvas
.
ds
.
params
or
not
augCanvas
.
ds
.
headers
:
return
def
getconfval
(
name
,
type
,
parselect
=
parselect
):
...
...
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