Offline analysis command options

[JakeWags]

Adds options to offline analysis command:

• --range: Standard deviation range for PCA [default: 3.0]
• --steps: Number of steps to use for PCA [default: 21]

[akenmorris]

The automated tests need updating:

 9: [  FAILED  ] 1 test, listed below:
9: [  FAILED  ] shapeworksTests.analyzeTest
9: 
9:  1 FAILED TEST
 9/10 Test  #9: shapeworksTests ..................***Failed   71.84 sec

[akenmorris]

2023-07-11T17:48:54.6862942Z 9: [ RUN      ] shapeworksTests.analyzeTest
2023-07-11T17:48:54.7366390Z 9: [2023-07-11 17:48:54.736] [info] Loading project: ellipsoid.swproj
2023-07-11T17:48:54.7400015Z 9: [2023-07-11 17:48:54.739] [info] Analyze::Analyze
2023-07-11T17:48:54.7400890Z 9: [2023-07-11 17:48:54.739] [info] number of subjects: 4
2023-07-11T17:48:54.7412695Z 9: [2023-07-11 17:48:54.740] [info] Computing stats...
2023-07-11T17:48:54.7413512Z 9: [2023-07-11 17:48:54.741] [info] number of shapes: 4
2023-07-11T17:48:54.7414324Z 9: [2023-07-11 17:48:54.741] [info] shape: ellipsoid_00
2023-07-11T17:48:54.7415127Z 9: [2023-07-11 17:48:54.741] [info] shape: ellipsoid_01
2023-07-11T17:48:54.7415921Z 9: [2023-07-11 17:48:54.741] [info] shape: ellipsoid_02
2023-07-11T17:48:54.7418203Z 9: [2023-07-11 17:48:54.741] [info] shape: ellipsoid_03
2023-07-11T17:48:54.7421973Z 9: [2023-07-11 17:48:54.741] [info] Computed stats successfully
2023-07-11T17:48:54.7479302Z 9: [2023-07-11 17:48:54.747] [info] ShapeWorks Offline Analysis
2023-07-11T17:48:54.7480481Z 9: [2023-07-11 17:48:54.747] [info] number of modes: 3
2023-07-11T17:48:54.7638461Z 9: [2023-07-11 17:48:54.763] [info] eigen value [0]: 336.20140083577616
2023-07-11T17:48:54.7639305Z 9: [2023-07-11 17:48:54.763] [info] explained_variance [0]: 95.86
2023-07-11T17:48:54.7640265Z 9: [2023-07-11 17:48:54.763] [info] cumulative_explained_variance [0]: 95.86
2023-07-11T17:48:54.8216501Z 9: [2023-07-11 17:48:54.820] [info] eigen value [1]: 11.20983907018731
2023-07-11T17:48:54.8217465Z 9: [2023-07-11 17:48:54.820] [info] explained_variance [1]: 3.20
2023-07-11T17:48:54.8218417Z 9: [2023-07-11 17:48:54.820] [info] cumulative_explained_variance [1]: 99.06
2023-07-11T17:48:54.8783283Z 9: [2023-07-11 17:48:54.877] [info] eigen value [2]: 3.310184050313001
2023-07-11T17:48:54.8784242Z 9: [2023-07-11 17:48:54.877] [info] explained_variance [2]: 0.94
2023-07-11T17:48:54.8785227Z 9: [2023-07-11 17:48:54.877] [info] cumulative_explained_variance [2]: 100.00
2023-07-11T17:48:54.9699368Z 9: 606,607c606,607
2023-07-11T17:48:54.9700279Z 9: <                     "pca_value": -0.30000001192092896,
2023-07-11T17:48:54.9701037Z 9: <                     "lambda": -5.50073890308563,
2023-07-11T17:48:54.9701785Z 9: ---
2023-07-11T17:48:54.9702398Z 9: >                     "pca_value": -0.4,
2023-07-11T17:48:54.9703056Z 9: >                     "lambda": -7.334318246007886,
2023-07-11T17:48:54.9703621Z 9: 609c609
2023-07-11T17:48:54.9704170Z 9: <                         "pca_mode_1_domain_0_minus_0.3.vtk"
2023-07-11T17:48:54.9704799Z 9: ---
2023-07-11T17:48:54.9705334Z 9: >                         "pca_mode_1_domain_0_minus_0.4.vtk"

Possibly the test output needs to be updated. Should the default execution be different?