Rcal 954 Remove jump code from rcal tree (#1534)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.gitignore

@@ -52,6 +52,10 @@ develop-eggs
 .installed.cfg
 distribute-*.tar.gz
 
+# emacs save files
+\#*
+.#*
+
 # Other
 .cache
 .tox

changes/1534.general.rst

@@ -0,0 +1 @@
+Remove the jump code for the deprecated jump detection for even ramps and update the documentation

docs/roman/associations/asn_from_list.rst

@@ -19,7 +19,7 @@ To create an association, use the following command:
 
  import romancal.associations.asn_from_list as asn_from_list
  product_name = 'test_product'
- items = {'r0000101001001001001_01101_0001_WFI01_uncal.asdf': 'science', 'r0000101001001001001_3_01101_0001_WFI01_uncal.asdf': 'guide_window', 'c': 'somethingelse'}
+ items = {'r0000101001001001001_0001_wfi01_uncal.asdf': 'science', 'r0000101001001001001_3_0001_wfi01_uncal.asdf': 'guide_window', 'c': 'somethingelse'}
  asn = asn_from_list.asn_from_list([(item, type_) for item, type_ in items.items()], product_name=product_name, with_exptype=True)
  asn['asn_rule']
  'DMS_ELPP_Base'
@@ -29,9 +29,9 @@ an example product that has both a science and guide window exposures
 would look like the following::
 
     asn['products']
-    [   {   'members': [   {   'expname': 'r0000101001001001001_01101_0001_WFI01_uncal.asdf',
+    [   {   'members': [   {   'expname': 'r0000101001001001001_0001_wfi01_uncal.asdf',
                                'exptype': 'science'},
-                           {   'expname': 'r0000101001001001001_3_01101_0001_WFI01_uncal.asdf',
+                           {   'expname': 'r0000101001001001001_3_0001_wfi01_uncal.asdf',
                                'exptype': 'guide_window'},
                            {'expname': 'c', 'exptype': 'somethingelse'}],
             'name': 'test_product'}]
@@ -41,7 +41,7 @@ To create a association with all the detectors for a given exposure from the com
 
 .. code-block:: python
 
-		asn_from_list -o detector_asn.json --product-name r0000101001001001001_01101_0001_WFI data/*_cal.asdf
+		asn_from_list -o detector_asn.json --product-name r0000101001001001001_0001_wfi data/*_cal.asdf
 
 where the individual calibrated detector files are in a data subdirectory.
 

docs/roman/data_products/file_naming.rst

@@ -11,7 +11,7 @@ The names of the exposure level data are constructed with information from the
 science header of the exposure, allowing users to map it to the observation in their corresponding
 APT files. The ASDF file naming scheme for the Exposure products is::
 
- r<ppppp><cc><aaa><sss><ooo><vvv>_<gg><s><aa>_<eeee>_<detector>_<prodType>.asdf
+ r<ppppp><cc><aaa><sss><ooo><vvv>_<eeee>_<detector>_<prodType>.asdf
 
 where
 
@@ -25,7 +25,7 @@ where
  - s: sequence ID (1=prime, >1 parallel)
  - aa: activity number (base 36)
  - eeee: exposure number
- - detector: detector name (e.g. WFI01, WFI02, ...)
+ - detector: detector name (e.g. wfi01, wfi02, ...)
  - prodType: product type identifier (e.g. 'uncal', 'cal')
 
 The standard <prodType> for the pipeline are uncal and cal, for the input products and resulting
@@ -35,8 +35,8 @@ linearity, jump, darkcurrent, rampfit, assignwcs, flat, and photom.
 
 An example Exposure Level 1 upcalibrated ASDF file name is::
 
- r0000101001001001001_01101_0001_WFI01_uncal.asdf
+ r0000101001001001001_0001_wfi01_uncal.asdf
 
 An example Exposure Level 2 product ASDF file name is::
 
- r0000101001001001001_01101_0001_WFI01_cal.asdf
+ r0000101001001001001_0001_wfi01_cal.asdf

docs/roman/datamodels/datamodels_asdf.rst

@@ -14,7 +14,7 @@ If you have installed the roman calibration pipeline you should also have access
 to the standalone tool asdfinfo which allows access to `ASDF <https://asdf-standard.readthedocs.io/>`_ (and roman) files
 from the terminal prompt,::
 
-    asdftool info r0000101001001001001_01101_0001_WFI16_cal.asdf
+    asdftool info r0000101001001001001_0001_wfi16_cal.asdf
     root (AsdfObject)
     ├─asdf_library (Software)
     │ ├─author (str): The ASDF Developers
@@ -62,10 +62,10 @@ To access the files via a python session,
 
     import roman_datamodels as rdm
     import asdf
-    with rdm.open('r0000101001001001001_01101_0001_WFI16_cal.asdf') as model:
+    with rdm.open('r0000101001001001001_0001_wfi16_cal.asdf') as model:
         <Manipulate the files>
 
-    with asdf.open('r0000101001001001001_01101_0001_WFI16_cal.asdf', memmap=False) as model:
+    with asdf.open('r0000101001001001001_0001_wfi16_cal.asdf', memmap=False) as model:
         <Manipulate the files>
 
 Once the files are loaded you can access various attributes. Below is a table
@@ -146,7 +146,7 @@ asdf tree.
 .. code:: python
 
     >>> from roman_datamodels import datamodels as rdm  # doctest: +SKIP
-    >>> d_uncal = rdm.open('r0000101001001001001_01101_0001_WFI01_uncal.asdf')  # doctest: +SKIP
+    >>> d_uncal = rdm.open('r0000101001001001001_0001_wfi01_uncal.asdf')  # doctest: +SKIP
     >>> d_uncal.info()  # doctest: +SKIP
     root (AsdfObject)
     ├─asdf_library (Software)

docs/roman/datamodels/models.rst

@@ -36,7 +36,7 @@ using python.
 .. testsetup::
     >>> from roman_datamodels import datamodels as rdm
     >>> from roman_datamodels.maker_utils import mk_datamodel
-    >>> fn = 'r0019106003005004023_03203_0034_WFI01_cal.asdf'
+    >>> fn = 'r0019106003005004023_0034_wfi01_cal.asdf'
     >>> image_model = mk_datamodel(rdm.ImageModel)
 
     # set some metadata for the below tests
@@ -46,7 +46,7 @@ using python.
 .. code-block:: python
 
     >>> from roman_datamodels import datamodels as rdm
-    >>> fn = 'r0019106003005004023_03203_0034_WFI01_cal.asdf'
+    >>> fn = 'r0019106003005004023_0034_wfi01_cal.asdf'
     >>> image_model = rdm.open(fn)  # doctest: +SKIP
     >>> type(image_model)
     <class 'roman_datamodels.datamodels._datamodels.ImageModel'>
@@ -145,7 +145,7 @@ You can examine the contents of your model from within python using
     meta.calibration_software_name	RomanCAL
     meta.calibration_software_version	9.9.0
        meta.product_type	l2
-           meta.filename	r0019106003005004023_03203_0034_WFI01_cal.asdf
+           meta.filename	r0019106003005004023_0034_wfi01_cal.asdf
           meta.file_date	2020-01-01T00:00:00.000
          meta.model_type	ImageModel
              meta.origin	STSCI/SOC

docs/roman/outlier_detection/main.rst

@@ -4,11 +4,13 @@ Description
 :Classes: `romancal.outlier_detection.OutlierDetectionStep`
 :Aliases: outlier_detection, outlier_detection_scaled, outlier_detection_stack
 
-Processing multiple datasets together allows for the identification of bad pixels
-or cosmic-rays that remain in each of the input images, many times at levels which
-were not detectable by the :ref:`jump <jump_step>` step. The ``outlier_detection`` step
-implements the following algorithm to identify and flag any remaining cosmic-rays or
-other artifacts left over from previous calibrations:
+Processing multiple datasets together allows for the identification of
+bad pixels or cosmic-rays that remain in each of the input images,
+many times at levels which were not detectable by jump detection in
+:ref:`ramp_fitting <ramp_fitting_step>` step.  The
+``outlier_detection`` step implements the following algorithm to
+identify and flag any remaining cosmic-rays or other artifacts left
+over from previous calibrations:
 
   - build a stack of input data
 

docs/roman/package_index.rst

@@ -7,7 +7,6 @@
    dq_init/index.rst
    flatfield/index.rst
    flux/index.rst
-   jump/index.rst
    linearity/index.rst
    outlier_detection/index.rst
    pipeline/index.rst

docs/roman/pipeline/exposure_pipeline.rst

@@ -43,11 +43,11 @@ The ``exposure`` pipeline has an optional argument::
 
   --use_ramp_jump_detection  boolean  default=True
 
-When set to ``True``, the pipeline will perform :ref:`jump <jump_step>`  detection as a part of the ramp
+When set to ``True``, the pipeline will perform jump detection as a part of the ramp
 fitting  step. The data at this stage of the pipeline are still in the form of the original
 3D ramps ( ngroups x ncols x nrows ) and have had all of the detector-level
 correction steps applied to it, up to but not including the detection and flagging of
-Cosmic-Ray (CR) hits within each ramp (integration). For this case the  :ref:`jump <jump_step>`
+Cosmic-Ray (CR) hits within each ramp (integration). For this case the  jump detection
 module in :ref:`ramp_fitting <ramp_fitting_step>` will update the dq array with the CR hits (jumps) that
 are identified in the step.
 
@@ -62,7 +62,7 @@ Inputs
 :File suffix: _uncal
 
 The input to the ``ExposurePipeline`` can be a single raw exposure,
-e.g. "r0008308002010007027_06311_0019_WFI01_uncal.asdf", which contains the
+e.g. "r0008308002010007027_0019_wfi01_uncal.asdf", which contains the
 original raw data from all of the detector readouts in the exposure
 ( ngroups x ncols x nrows ). The raw data may also be input using an association file.
 

docs/roman/pipeline/mosaic_pipeline.rst

@@ -54,7 +54,7 @@ An association of 2D calibrated image data
 :File suffix: _cal
 
 The input to the ``MosaicPipeline`` is a group of calibrated exposures,
-e.g. "r0008308002010007027_06311_0019_WFI01_cal.asdf", which contains the
+e.g. "r0008308002010007027_0019_wfi01_cal.asdf", which contains the
 calibrated data for the the exposures. The most convenient way to pass the list of
 exposures to be processed with the mosaic level pipeline is to use an association.
 Instructions on how to create an input association an be found at :ref:`asn-from-list`.

docs/roman/pipeline_naming_conventions.rst

@@ -47,10 +47,10 @@ name. If the input file name already has a known suffix, that suffix
 will be replaced. For example:
 ::
 
-   $ strun romancal.dq_init.DQInitStep r0008308002010007027_06311_0019_WFI01_uncal.asdf
+   $ strun romancal.dq_init.DQInitStep r0008308002010007027_0019_wfi01_uncal.asdf
 
 produces an output file named
-``r0008308002010007027_06311_0019_WFI01_dq_init.asdf``.
+``r0008308002010007027_0019_wfi01_dq_init.asdf``.
 
 
 .. _pipeline_step_suffix_definitions: