Skip to content
This repository has been archived by the owner on Jul 29, 2023. It is now read-only.

Inference bug, pandas docker version #153

Merged
merged 6 commits into from
Jun 17, 2022
Merged

Inference bug, pandas docker version #153

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
db8ee0e
fix channel_name bug
JohannaRahm Jun 3, 2022
2d2cb8c
set pandas to 0.24.2 in docker requirements
JohannaRahm Jun 3, 2022
e09adea
add test & update docstring for aux_utils - get_sms_im_name function
JohannaRahm Jun 16, 2022
c1cbb1d
refactor aux utils test
JohannaRahm Jun 16, 2022
1326aaf
change channel_name if statement to cover NaN
JohannaRahm Jun 16, 2022
79d714c
split tests in two functions
JohannaRahm Jun 17, 2022
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
6 changes: 3 additions & 3 deletions micro_dl/utils/aux_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -184,7 +184,7 @@ def get_sms_im_name(time_idx=None,
This function is custom for the computational microscopy (SMS)
group, who has the following file naming convention:
File naming convention is assumed to be:
img_channelname_t***_p***_z***.tif
img_channelname_t***_p***_z***_extrafield.tif
This function will alter list and dict in place.

:param int time_idx: Time index
Expand All @@ -194,11 +194,11 @@ def get_sms_im_name(time_idx=None,
:param str extra_field: Any extra string you want to include in the name
:param str ext: Extension, e.g. '.png'
:param int int2str_len: Length of string of the converted integers
:return st im_name: Image file name
:return str im_name: Image file name
"""

im_name = "img"
if np.isnan(channel_name):
if not pd.isnull(channel_name):
im_name += "_" + str(channel_name)
if time_idx is not None:
im_name += "_t" + str(time_idx).zfill(int2str_len)
Expand Down
2 changes: 1 addition & 1 deletion requirements_docker.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ natsort==6.0.0
nose==1.3.7
numpy==1.21.0
opencv-python==4.4.0.40
pandas==1.1.5
pandas==0.24.2
jennyfolkesson marked this conversation as resolved.
Show resolved Hide resolved
protobuf==3.20.1
pydot==1.4.1
PyYAML>=5.4
Expand Down
26 changes: 26 additions & 0 deletions tests/utils/aux_utils_tests.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -95,6 +95,32 @@ def test_get_im_name():
nose.tools.assert_equal(im_name, 'im_c2_z3_t1_p4_hej.png')


def test_get_sms_im_name():
im_name = aux_utils.get_sms_im_name(
time_idx=0,
channel_name='phase',
slice_idx=10,
pos_idx=100,
extra_field='blub',
ext='.png',
int2str_len=3,
)
nose.tools.assert_equal(im_name, 'img_phase_t000_p100_z010_blub.png')


def test_get_sms_im_name_nones():
im_name = aux_utils.get_sms_im_name(
time_idx=0,
channel_name=None,
slice_idx=None,
pos_idx=10,
extra_field=None,
ext='.jpg',
int2str_len=2,
)
nose.tools.assert_equal(im_name, 'img_t00_p10.jpg')


Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🥇
Great job adding tests! My only comment is that I would separate these into two tests, which makes it easier to spot exactly where the code breaks if a test isn't passing. But that's optional.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

done!

def test_get_im_name_default():
im_name = aux_utils.get_im_name()
nose.tools.assert_equal(im_name, 'im.png')
Expand Down