Switch to using Param and SHARED_PARAMS as much as possible (#161)

* Switch to using Param and SHARED_PARAMS as much as possible

* updated params in table_tools.py

src/rail/core/common_params.py

@@ -30,6 +30,7 @@
     hdf5_groupname=Param(
         str, "photometry", msg="name of hdf5 group for data, if None, then set to ''"
     ),
+    chunk_size=Param(int, 10000, msg="Number of object per chunk for parallel processing"),
     zmin=Param(float, 0.0, msg="The minimum redshift of the z grid"),
     zmax=Param(float, 3.0, msg="The maximum redshift of the z grid"),
     nzbins=Param(int, 301, msg="The number of gridpoints in the z grid"),

src/rail/creation/degrader.py

@@ -4,6 +4,7 @@
 and returns a pandas DataFrame, and wraps the run method.
 """
 
+from ceci.config import StageParameter as Param
 from rail.core.stage import RailStage
 from rail.core.data import PqHandle
 
@@ -19,7 +20,9 @@ class Degrader(RailStage):  # pragma: no cover
 
     name = "Degrader"
     config_options = RailStage.config_options.copy()
-    config_options.update(seed=12345)
+    config_options.update(
+        seed=Param(int, default=12345, msg="Random number seed"),
+    )
     inputs = [("input", PqHandle)]
     outputs = [("output", PqHandle)]
 

src/rail/creation/degraders/quantityCut.py

@@ -2,6 +2,7 @@
 
 from numbers import Number
 
+from ceci.config import StageParameter as Param
 import numpy as np
 from rail.creation.selector import Selector
 
@@ -15,7 +16,9 @@ class QuantityCut(Selector):
 
     name = "QuantityCut"
     config_options = Selector.config_options.copy()
-    config_options.update(cuts=dict)
+    config_options.update(
+        cuts=Param(dict, required=True, msg="Cuts to apply"),
+    )
 
     def __init__(self, args, **kwargs):
         """Constructor.

src/rail/creation/engine.py

@@ -6,6 +6,7 @@
 """
 
 import qp
+from ceci.config import StageParameter as Param
 from rail.core.data import DataHandle, ModelHandle, QPHandle, TableHandle
 from rail.core.stage import RailStage
 
@@ -15,7 +16,9 @@ class Modeler(RailStage):  # pragma: no cover
 
     name = "Modeler"
     config_options = RailStage.config_options.copy()
-    config_options.update(seed=12345)
+    config_options.update(
+        seed=Param(int, default=12345, msg="Random number seed"),
+    )
     inputs = [("input", DataHandle)]
     outputs = [("model", ModelHandle)]
 
@@ -52,7 +55,10 @@ class Creator(RailStage):  # pragma: no cover
 
     name = "Creator"
     config_options = RailStage.config_options.copy()
-    config_options.update(n_samples=int, seed=12345)
+    config_options.update(
+        n_samples=Param(int, required=True, msg="Number of samples to create"),
+        seed=Param(int, default=12345, msg="Random number seed"),
+    )
     inputs = [("model", ModelHandle)]
     outputs = [("output", TableHandle)]
 
@@ -137,7 +143,9 @@ class PosteriorCalculator(RailStage):  # pragma: no cover
 
     name = "PosteriorCalculator"
     config_options = RailStage.config_options.copy()
-    config_options.update(column=str)
+    config_options.update(
+        column=Param(str, required=True, msg="Column to compute posterior for"),
+    )
     inputs = [
         ("model", ModelHandle),
         ("input", TableHandle),

src/rail/estimation/algos/true_nz.py

@@ -22,8 +22,8 @@ class TrueNZHistogrammer(RailStage):
         nzbins=SHARED_PARAMS,
         redshift_col=SHARED_PARAMS,
         selected_bin=Param(int, -1, msg="Which tomography bin to consider"),
-        chunk_size=10000,
-        hdf5_groupname="",
+        chunk_size=SHARED_PARAMS,
+        hdf5_groupname=SHARED_PARAMS,
     )
     inputs = [("input", TableHandle), ("tomography_bins", TableHandle)]
     outputs = [("true_NZ", QPHandle)]

src/rail/estimation/classifier.py

@@ -4,6 +4,7 @@
 
 import gc
 from rail.core.data import QPHandle, TableHandle, ModelHandle, Hdf5Handle
+from rail.core.common_params import SHARED_PARAMS
 from rail.core.stage import RailStage
 
 
@@ -19,7 +20,10 @@ class CatClassifier(RailStage):  # pragma: no cover
 
     name = "CatClassifier"
     config_options = RailStage.config_options.copy()
-    config_options.update(chunk_size=10000, hdf5_groupname=str)
+    config_options.update(
+        chunk_size=SHARED_PARAMS,
+        hdf5_groupname=SHARED_PARAMS,
+    )
     inputs = [("model", ModelHandle), ("input", TableHandle)]
     outputs = [("output", TableHandle)]
 
@@ -102,7 +106,7 @@ class PZClassifier(RailStage):
 
     name = "PZClassifier"
     config_options = RailStage.config_options.copy()
-    config_options.update(chunk_size=10000)
+    config_options.update(chunk_size=SHARED_PARAMS)
     inputs = [("input", QPHandle)]
     outputs = [("output", Hdf5Handle)]
 

src/rail/estimation/estimator.py

@@ -28,7 +28,7 @@ class CatEstimator(RailStage, PointEstimationMixin):
     name = "CatEstimator"
     config_options = RailStage.config_options.copy()
     config_options.update(
-        chunk_size=Param(dtype=int, default=10000),
+        chunk_size=SHARED_PARAMS,
         hdf5_groupname=SHARED_PARAMS,
         zmin=SHARED_PARAMS,
         zmax=SHARED_PARAMS,

src/rail/estimation/summarizer.py

@@ -5,6 +5,7 @@
 import numpy as np
 
 from rail.core.data import QPHandle, TableHandle, ModelHandle
+from rail.core.common_params import SHARED_PARAMS
 from rail.core.stage import RailStage
 
 # for backwards compatibility
@@ -22,7 +23,7 @@ class CatSummarizer(RailStage):
 
     name = "CatSummarizer"
     config_options = RailStage.config_options.copy()
-    config_options.update(chunk_size=10000)
+    config_options.update(chunk_size=SHARED_PARAMS)
     inputs = [("input", TableHandle)]
     outputs = [("output", QPHandle)]
 
@@ -66,7 +67,7 @@ class PZSummarizer(RailStage):
 
     name = "PZtoNZSummarizer"
     config_options = RailStage.config_options.copy()
-    config_options.update(chunk_size=10000)
+    config_options.update(chunk_size=SHARED_PARAMS)
     inputs = [("model", ModelHandle), ("input", QPHandle)]
     outputs = [("output", QPHandle)]
 
@@ -129,7 +130,7 @@ class SZPZSummarizer(RailStage):
 
     name = "SZPZtoNZSummarizer"
     config_options = RailStage.config_options.copy()
-    config_options.update(chunk_size=10000)
+    config_options.update(chunk_size=SHARED_PARAMS)
     inputs = [
         ("input", TableHandle),
         ("spec_input", TableHandle),

src/rail/tools/table_tools.py

@@ -2,6 +2,7 @@
 
 import tables_io
 
+from ceci.config import StageParameter as Param
 from rail.core.stage import RailStage
 
 from rail.core.data import PqHandle, Hdf5Handle
@@ -21,7 +22,10 @@ class ColumnMapper(RailStage):
 
     name = "ColumnMapper"
     config_options = RailStage.config_options.copy()
-    config_options.update(chunk_size=100_000, columns=dict, inplace=False)
+    config_options.update(
+        columns=Param(dict, required=True, msg="Map of columns to rename"),
+        inplace=Param(bool, default=False, msg="Update file in place"),
+    )
     inputs = [("input", PqHandle)]
     outputs = [("output", PqHandle)]
 
@@ -70,7 +74,10 @@ class RowSelector(RailStage):
 
     name = "RowSelector"
     config_options = RailStage.config_options.copy()
-    config_options.update(start=int, stop=int)
+    config_options.update(
+        start=Param(int, required=True, msg="Starting row number"),
+        stop=Param(int, required=True, msg="Stoppig row number"),
+    )                       
     inputs = [("input", PqHandle)]
     outputs = [("output", PqHandle)]
 
@@ -112,7 +119,9 @@ class TableConverter(RailStage):
 
     name = "TableConverter"
     config_options = RailStage.config_options.copy()
-    config_options.update(output_format=str)
+    config_options.update(
+        output_format=Param(str, required=True, msg="Format of output table"),
+    )
     inputs = [("input", PqHandle)]
     outputs = [("output", Hdf5Handle)]