piescope v0.2.0 #58

patrickcleeve2 · 2022-03-25T00:18:18Z

This pull request upgrade piescope to version 0.2.0.

Features include:

Improved multithreaded performance for live imaging.
Added Hammamatsu camera support
Volumetric Imaging
fibsem package integration

Requires:

piescope_gui==0.2.0

Co-authored-by: DavidDierickx <[email protected]>

pep8speaks · 2022-03-25T06:04:20Z

Hello @patrickcleeve2! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file piescope/correlation.py:

Line 128:80: E501 line too long (83 > 79 characters)
Line 134:80: E501 line too long (103 > 79 characters)
Line 154:80: E501 line too long (88 > 79 characters)

In the file piescope/fibsem.py:

Line 17:1: E302 expected 2 blank lines, found 1
Line 25:1: W293 blank line contains whitespace
Line 33:80: E501 line too long (105 > 79 characters)
Line 39:29: E231 missing whitespace after ':'
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Line 305:80: E501 line too long (83 > 79 characters)
Line 306:80: E501 line too long (84 > 79 characters)

In the file piescope/lm/arduino.py:

Line 9:1: E302 expected 2 blank lines, found 1
Line 17:76: E261 at least two spaces before inline comment
Line 17:80: E501 line too long (91 > 79 characters)
Line 20:62: E226 missing whitespace around arithmetic operator

In the file piescope/lm/dcam/dcam.py:

Line 5:80: E501 line too long (94 > 79 characters)
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Line 624:80: E501 line too long (86 > 79 characters)
Line 634:5: E303 too many blank lines (2)
Line 636:5: E301 expected 1 blank line, found 0
Line 689:80: E501 line too long (84 > 79 characters)

In the file piescope/lm/dcam/dcam_live_capturing.py:

Line 35:1: W293 blank line contains whitespace
Line 63:80: E501 line too long (84 > 79 characters)
Line 69:80: E501 line too long (87 > 79 characters)
Line 73:80: E501 line too long (103 > 79 characters)
Line 78:80: E501 line too long (81 > 79 characters)
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Line 97:80: E501 line too long (90 > 79 characters)
Line 100:80: E501 line too long (84 > 79 characters)
Line 102:80: E501 line too long (82 > 79 characters)

In the file piescope/lm/dcam/dcam_show_device_list.py:

Line 39:80: E501 line too long (82 > 79 characters)

In the file piescope/lm/dcam/dcam_show_properties.py:

Line 14:1: E302 expected 2 blank lines, found 1
Line 21:1: W293 blank line contains whitespace
Line 35:80: E501 line too long (84 > 79 characters)
Line 37:80: E501 line too long (82 > 79 characters)

In the file piescope/lm/dcam/dcam_show_single_captured_image.py:

Line 62:80: E501 line too long (87 > 79 characters)
Line 74:80: E501 line too long (91 > 79 characters)
Line 77:80: E501 line too long (93 > 79 characters)
Line 81:80: E501 line too long (90 > 79 characters)
Line 84:80: E501 line too long (84 > 79 characters)
Line 86:80: E501 line too long (82 > 79 characters)

In the file piescope/lm/dcam/dcamapi4.py:

Line 28:80: E501 line too long (81 > 79 characters)
Line 29:80: E501 line too long (81 > 79 characters)
Line 31:80: E501 line too long (85 > 79 characters)
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Line 143:5: E303 too many blank lines (2)
Line 147:80: E501 line too long (81 > 79 characters)
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Line 602:1: E303 too many blank lines (3)
Line 1038:1: E302 expected 2 blank lines, found 1
Line 1089:80: E501 line too long (87 > 79 characters)

In the file piescope/lm/detector.py:

Line 14:1: E302 expected 2 blank lines, found 1
Line 22:80: E501 line too long (94 > 79 characters)
Line 23:80: E501 line too long (88 > 79 characters)
Line 54:80: E501 line too long (84 > 79 characters)
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Line 154:1: W293 blank line contains whitespace
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Line 167:35: W291 trailing whitespace
Line 168:1: W293 blank line contains whitespace

In the file piescope/lm/laser.py:

Line 54:80: E501 line too long (125 > 79 characters)
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Line 80:1: W293 blank line contains whitespace
Line 83:80: E501 line too long (100 > 79 characters)
Line 88:5: E303 too many blank lines (2)
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Line 108:80: E501 line too long (88 > 79 characters)
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In the file piescope/lm/mirror.py:

Line 6:19: E226 missing whitespace around arithmetic operator
Line 6:31: E226 missing whitespace around arithmetic operator
Line 7:20: E226 missing whitespace around arithmetic operator
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Line 9:1: E302 expected 2 blank lines, found 1
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Line 21:1: E302 expected 2 blank lines, found 1
Line 47:61: E226 missing whitespace around arithmetic operator
Line 75:80: E501 line too long (91 > 79 characters)
Line 79:80: E501 line too long (81 > 79 characters)

In the file piescope/lm/objective.py:

Line 43:80: E501 line too long (93 > 79 characters)

In the file piescope/lm/structured.py:

Line 43:21: E226 missing whitespace around arithmetic operator
Line 56:23: E226 missing whitespace around arithmetic operator
Line 57:22: E226 missing whitespace around arithmetic operator
Line 58:21: E226 missing whitespace around arithmetic operator
Line 59:23: E226 missing whitespace around arithmetic operator

In the file piescope/lm/volume.py:

Line 14:80: E501 line too long (84 > 79 characters)
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In the file piescope/utils.py:

Line 108:9: E122 continuation line missing indentation or outdented
Line 109:9: E122 continuation line missing indentation or outdented
Line 125:80: E501 line too long (98 > 79 characters)
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Line 154:5: E265 block comment should start with '# '
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Line 211:1: E302 expected 2 blank lines, found 1
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Comment last updated at 2022-07-04 03:43:31 UTC

… develop

Phases

Hamamatsu

GenevieveBuckley and others added 30 commits February 13, 2020 14:49

Increment version number for development

ac2026e

Added structured fill, pulse function for single and multi lines

f5adbcb

Changed volume function to work with TTL

c0d476b

Fixed nidaqmx importing

f6ff1e4

Added hardware triggering for camera_grab

07952f6

Added nidaqmx to requirements

9daeb5a

Fixed references to nidaqmx

83840f8

Minor spacing fix

52853b0

Fixed function calls

7bb283d

removed unused import

3319fde

Fixed camera_grab parameters

26a5706

Removed unecessary prints

2ece58e

Delay given in us, changed division factor to match

ae77043

Changed laser_name to pin for multi_pulse

d3c6601

Small documentation fixes

74b92bd

Implemented hardware triggering as default

34dc4a6

Changed volume shape to include patterns

720d07d

Changed laser and camera pins

8b7123a

Added single_line_onoff function for pattern

d02843e

Forced negative laser power to 0, >100 power to 100

e0ff56c

update to github

fd702b9

NIcontroller python

113f687

removed incorrect import

a830627

added arduino and PIStage controls

dd9ec6b

fixed calibrations for mirror/shift

4db9624

refactored laser.py

e0ba5eb

remove unused initialise_laser function

cda96ec

remove internal path dependence

9c6a308

remove config path creation

546e46a

add ip and offline to config

adf1883

DavidDierickx and others added 8 commits March 9, 2022 17:08

refactored correlation

fbb3eed

Updated save, YOLO, TODO

8610dac

lower indentation in save images

7379398

fixed stage movement, added gui elems to dataclass

491f526

Co-authored-by: DavidDierickx <[email protected]>

fixed milling currents, error window

91f48f9

fix volume imaging

07a0d3d

integrate the guis

a49dd0b

Co-authored-by: DavidDierickx <[email protected]>

fixed last fib image type issue

dd4490b

patrickcleeve2 requested a review from DavidDierickx March 25, 2022 00:18

conf update

8bfb042

DavidDierickx and others added 18 commits April 7, 2022 17:14

Fixed volume saving notes

2990f18

updates

eee6554

Merge branch 'develop' of https://github.com/DeMarcoLab/piescope into…

c3a5d6b

… develop

updated phase calculations (hardware)

97d4218

remove old volume acquisition function

86a78f5

add phase selection

23146b8

updated phase movements

52b7d3c

Merge pull request #61 from DeMarcoLab/phases

8cd31f3

Phases

change to piescope filing

12c6731

updated stage shift

995c14f

add dcam API

7f8d275

add Hamamatsu Class

45f17eb

Add close_camera function

2a26f95

need for speed

d27470b

updated for hammatsu

65af18a

[FEAT] add zoom for light imaging

ab73e13

cleanup

93b9a5f

Merge pull request #66 from DeMarcoLab/hamamatsu

0040e7c

Hamamatsu

patrickcleeve2 marked this pull request as draft August 15, 2022 23:17

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piescope v0.2.0 #58

piescope v0.2.0 #58

patrickcleeve2 commented Mar 25, 2022 •

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Comment last updated at 2022-07-04 03:43:31 UTC

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