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SAS Dashboard

Represent and analyse your Small Angle Scattering (SAS) data.

README: English, 中文

环境依赖

使用 pip 安装依赖的库:

pip install -r requirements.txt

使用 conda 环境:

conda install --file requirements.txt

使用指南

python run.py /path/to/experiment-setup-1.yml /path/to/another-experiment-setup-2.yml

实验配置文件示例 SSRF-MagR-201805.yml:

project_name: MagR
experiment_name: SSRF-MagR-201805
experiment_facility: SSRF
experiment_date: May 04~05, 2018
participants: Haiguang Liu, Can Xie, Peiling Yang, Yingchen Shi, Lanqing Huang, Siyin Qin, Zhen Guo, Xiaotian Wang
description: Description, comments or summary for this experiment

# sample_list:  # useless for now

root_path: /path/to/SSRF/SSRF-MagR-201805/Analysis/Experiments
# or
root_path: ['Day_1_data', 'Day_2_data']
# or
root_path:
    - 'Day_1_data'
    - 'Day_2_data'

default_raw_cfg: '20180503-recentering-remasking'
raw_cfg:
    '20180503':
        cfg_path: ???
        mask_npy: ???
        MaskDimension: (1043, 981)
        Xcenter: ???
        Ycenter: ???
    '20180503-recentering-remasking':
        cfg_path: path/to/SSRF-MagR-201805/cfg/20180503-recentering-remasking.cfg
        mask_npy: path/to/SSRF-MagR-201805/cfg/20180503-recentering-remasking-BeamStopMask.npy
        MaskDimension: (1043, 981)
        Xcenter: 359
        Ycenter: 914

图像的实际中心为:

(row_center, col_center) = (MaskDimension[0] - Ycenter, Xcenter)

RAW 配置鉴于有可能会有多个 RAW 的配置文件 .cfg，因此可以通过 default_raw_cfg 设定默认的 RAW 配置文件。当需要获取特定 run 的 RAW 配置时会去 run 文件夹里的 config.yml 中寻找 raw_cfg 设置，如果不存在 raw_cfg 的信息就将使用默认的 default_raw_cfg。

组织结构

Project 由 Experiment 组成，Experiment 由 Run 组成。每个 Run 包含每次的采集的实验数据。

Project-Name (eg: 'MagR')
|- project_settings.yml
|- Experiment-1 (eg: 'SSRF-MagR-201803')
   |- expperiment-settings-1.yml
   |- Run-1 (eg: EXP01)
   |- Run-2 (eg: EXP02)
      |- Processed
      ...
      |- Subtracted
      |- config.yml
      |- setup.yml
   |- Run-3
   ...
   |- Run-39
   |- Run-40
|- Experiment-2 (eg: 'SSRF-MagR-201805')
   |- experiment-settings-2.yml
   |- Run-01
   |- Run-02
   ...
   |- Run-49
   |- Run-50

在 experiment-settings-1.yml 中设定好 root_path 后，sasdash 会遍历 root_path 中的所有子目录去寻找所有的 setup.yml，默认将使用 setup.yml 所在的目录视为单个 run 的根目录。

setup.yml 示例:

number: 27
sample: nano magnetic beads
concentration: 1.0 # mg/ml
magnetic_field: True
magnet_distance: None / 60 # mm
duration: 6 # minuntes
exposure_mode: automatic
exposure_time: 1.0 # second / per frame
frames: 40
description: None
extra_info: None
simple_conclusion: Undone

可以添加更多有效详细的信息。