matrixscreener 0.6.1

功能

• 作为python对象访问实验
• 压缩到PNG而不丢失精度、元数据或颜色映射
• ImageJ缝合（斐济通过 fijibin页）
• 通过CAM TCP/IP插座与显微镜通信

安装

pip install matrixscreener

示例

缝合实验

importmatrixscreener# create short handExperiment=matrixscreener.experiment.Experiment# path should contain AditionalData and slide--S*scan=Experiment('path/to/experiment')print(matrixscreener.imagej._bin)# Fiji installed via package fijibinmatrixscreener.imagej._bin='/path/to/imagej'# if path is omitted, experiment path is used for output filesstitched_images=experiment.stitch('/path/to/output/files/')

缝合特定井

frommatrixscreenerimportexperiment# path should contain AditionalData and slide--S*stitched_images=experiment.stitch('/path/to/well')

对所有图像执行操作

frommatrixscreenerimportexperimentscan=experiment.Experiment('path/to/experiment--')forimageinscan.images:dostuff...

在特定的井/田上做事

frommatrixscreenerimportexperiment# select specific partsselected_wells=[wellforwellinscan.wellsif'U00'inwell]forwellinselected_wells:dostuff...defcondition(path):x_above=experiment.attribute(path,'X')>1x_below=experiment.attribute(path,'X')<5returnx_aboveandx_belowselected_fields=[fieldforfieldinscan.fieldsifcondition(field)]forfieldinselected_fields:dostuff..

减去数据

frommatrixscreener.experimentimportattribute# get all channelschannels=[attribute(image,'C')forimageinscan.images]min_ch,max_ch=min(channels),max(channels)

与显微镜通信

frommatrixscreener.camimportCAMcam=CAM()# initiate and connect, default localhost:8895# some commands are created as short hands# start matrix scanresponse=cam.start_scan()print(response)# but you could also create your own command with a list of tuplescommand=[('cmd','enableall'),('value','true')]response=cam.send(command)print(response)# or even send it as a bytes string (note the b)command=b'/cmd:enableall /value:true'response=cam.send(command)print(response)

批量无损压缩实验

import matrixscreener as ms

e = ms.experiment.Experiment('/path/to/experiment')
pngs = ms.experiment.compress(e.images)
print(pngs)

另请参见this notebook。

发展

git clone https://github.com/arve0/matrixscreener.git
cd matrixscreener
# hack
./setup.py install

测试

pip install tox
tox

特定测试，这里是压缩测试

pip install pytest numpy
py.test -k compression tests/test_experiment.py

具有额外输出的特定测试，出错时跳转到pdb

DEBUG=matrixscreener py.test -k compression tests/test_experiment.py --pdb -s

API参考

所有命令都应记录在numpy format中的docstrings中。

API引用可用 online，可以用 pydoc或任何 用docstring自动完成的编辑器/repl。

例如：

pydoc matrixscreener
pydoc matrixscreener.cam
pydoc matrixscreener.experiment
pydoc matrixscreener.imagej

释放程序

• 创建 .pypirc 如果不见了。

  [distutils]
  index-servers=
          pypi
          pypitest
  
  [pypitest]
  repository = https://testpypi.python.org/pypi
  username = username
  password = password
  
  [pypi]
  repository = https://pypi.python.org/pypi
  username = username
  password = password
  

• 更新changelog.md

• 在__init__.py、setup.py和doc/conf.py中更新版本

• Git提交和标记版本

• ./generate-rst.sh（需要pandoc）

• 阶段发布： python setup.py sdist bdist_wheel upload -r pypitest

• 发布：python setup.py sdist bdist_wheel upload