Readers: polarization from miniCBF and d*TREK headers (RESULT-CHANGING)

No reader parsed a polarization, and ApplyRugnuxExperimentDefaults then set
P = 0.99 (an undulator value) unconditionally, so laboratory-source data were
corrected as if from a synchrotron. Every d*TREK (Rigaku Saturn/A200) header in
the open arm states SOURCE_POLARZ=0.5 1 0 0, i.e. unpolarized; at Cu K-alpha and
2 A the wrong factor puts a +-33% azimuthal modulation on the intensities.

- d*TREK SMV: SOURCE_POLARZ is the fraction f followed by the plane normal (as
  dxtbx's FormatSMVRigaku reads it); stored as degree 2f - 1, negative where the
  normal lies along lab x (plane containing y).
- miniCBF: "# Polarization f" is the fraction in the horizontal plane; stored as
  2f - 1 ("None" or a missing line leave it unset).
- ApplyRugnuxExperimentDefaults sets 0.99 only where the file stated none;
  --polarization still overrides. ADSC SMV, marCCD and NXmx state nothing and
  keep 0.99.
- The "Header:" log line reports the stated polarization.

RESULT-CHANGING: d*TREK home-source sets (0.99 -> 0), one Rigaku miniCBF set
(0.99 -> 0), miniCBF sets stating 0.99 (0.99 -> 0.98).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4

tests/JFJochReaderTest.cpp

@@ -4049,6 +4049,33 @@ namespace {
     }
 }
 
+TEST_CASE("JFJochCBFReader_Polarization", "[HDF5][Full][portable]") {
+    const int64_t nx = 24, ny = 16;
+    // The line states the fraction polarized in the horizontal plane; the correction wants the degree.
+    WriteMiniCBFSweep("cbfpol", "# Polarization 0.990\n", nx, ny);
+    JFJochCBFReader reader;
+    REQUIRE_NOTHROW(reader.ReadFiles("cbfpol_0001.cbf"));
+    REQUIRE(reader.GetDataset()->experiment.GetPolarizationFactor().has_value());
+    CHECK(reader.GetDataset()->experiment.GetPolarizationFactor().value() == Catch::Approx(0.98));
+    reader.Close();
+    RemoveMiniCBFSweep("cbfpol");
+
+    WriteMiniCBFSweep("cbfunpol", "# Polarization   0.500000\n", nx, ny);   // a laboratory tube
+    JFJochCBFReader lab;
+    REQUIRE_NOTHROW(lab.ReadFiles("cbfunpol_0001.cbf"));
+    REQUIRE(lab.GetDataset()->experiment.GetPolarizationFactor().has_value());
+    CHECK(lab.GetDataset()->experiment.GetPolarizationFactor().value() == Catch::Approx(0.0).margin(1e-6));
+    lab.Close();
+    RemoveMiniCBFSweep("cbfunpol");
+
+    WriteMiniCBFSweep("cbfnopol", "# Polarization None\n", nx, ny);
+    JFJochCBFReader none;
+    REQUIRE_NOTHROW(none.ReadFiles("cbfnopol_0001.cbf"));
+    CHECK_FALSE(none.GetDataset()->experiment.GetPolarizationFactor().has_value());
+    none.Close();
+    RemoveMiniCBFSweep("cbfnopol");
+}
+
 TEST_CASE("JFJochCBFReader_AxisTableStatesTheMounting", "[HDF5][Full][portable]") {
     const int64_t nx = 24, ny = 16;
 
@@ -4553,6 +4580,7 @@ TEST_CASE("JFJochSMVReader_Geometry", "[HDF5][Full][portable]") {
         REQUIRE(x.GetGoniometer().has_value());
         CHECK(x.GetGoniometer()->GetStart_deg() == Catch::Approx(5.0));
         CHECK(x.GetGoniometer()->GetIncrement_deg() == Catch::Approx(0.2));
+        CHECK_FALSE(x.GetPolarizationFactor().has_value());   // an ADSC header states none
         reader.Close();
         RemoveSMVSweep("smv_", ".img");
     }
@@ -4572,7 +4600,8 @@ TEST_CASE("JFJochSMVReader_Geometry", "[HDF5][Full][portable]") {
           << "CCD_GONIO_VECTORS=0 0 1  1 0 0  0 1 0  1 0 0  0 1 0  0 0 -1;\n"
           << "ROTATION=-13.500  -13.000 0.500  30.000 0.000 0.000 0.000  100.000 0.000 0.000;\n"
           << "ROTATION_AXIS_NAME=Omega;\nROTATION_VECTOR=1.000 0.000 0.000;\n"
-          << "SOURCE_WAVELENGTH=1.000000  1.541780;\nSATURATED_VALUE=4194176;\nRAXIS_COMPRESSION_RATIO=128;\n}\n";
+          << "SOURCE_WAVELENGTH=1.000000  1.541780;\nSATURATED_VALUE=4194176;\nRAXIS_COMPRESSION_RATIO=128;\n"
+          << "SOURCE_POLARZ=0.9000 1.0000 0.0000 0.0000;\n}\n";
         std::string head = h.str();
         head.resize(1024, ' ');
         std::vector<uint16_t> pixels(static_cast<size_t>(nx) * ny, 100);
@@ -4613,6 +4642,10 @@ TEST_CASE("JFJochSMVReader_Geometry", "[HDF5][Full][portable]") {
         CHECK(x.GetGoniometer()->GetStart_deg() == Catch::Approx(-13.5));
         CHECK(x.GetGoniometer()->GetIncrement_deg() == Catch::Approx(0.5));
         CHECK((x.GetGoniometer()->GetAxis() - Coord(1, 0, 0)).Length() < 1e-5f);
+        // A fraction of 0.9 is a degree of 0.8; the plane's normal along x puts the plane on y, which
+        // the correction spells as a negative degree.
+        REQUIRE(x.GetPolarizationFactor().has_value());
+        CHECK(x.GetPolarizationFactor().value() == Catch::Approx(-0.8));
         reader.Close();
         remove("dtrek_0001.img");
     }