OpenREM 1.0.0b2__py3-none-any.whl → 1.0.0b3__py3-none-any.whl

openrem/remapp/tests/test_export_mammo_csv.py

@@ -1,242 +1,242 @@
-# This Python file uses the following encoding: utf-8
-# test_export_mammo_csv.py
-
-from builtins import range  # pylint: disable=redefined-builtin
-import os
-from collections import Counter
-from django.contrib.auth.models import User, Group
-from django.test import TestCase, RequestFactory
-from remapp.extractors import mam, rdsr
-from remapp.exports.mg_export import exportMG2excel
-from remapp.exports.mg_csv_nhsbsp import mg_csv_nhsbsp
-from remapp.models import PatientIDSettings, Exports
-
-
-class ExportMammoCSV(TestCase):
-    def setUp(self):
-        self.factory = RequestFactory()
-        self.user = User.objects.create_user(
-            username="jacob", email="jacob@…", password="top_secret"
-        )
-        eg = Group(name="exportgroup")
-        eg.save()
-        eg.user_set.add(self.user)
-        eg.save()
-
-        PatientIDSettings.objects.create()
-
-        dicom_file = os.path.join("test_files", "MG-Im-GE-SenDS-scaled.dcm")
-        root_tests = os.path.dirname(os.path.abspath(__file__))
-        dicom_path = os.path.join(root_tests, dicom_file)
-
-        mam.mam(dicom_path)
-
-    def test_all_values(self):
-        import pandas as pd
-
-        filter_set = {}
-        pid = False
-        name = False
-        patient_id = False
-
-        exportMG2excel(filter_set, pid=pid, name=name, patid=patient_id, user=self.user)
-
-        task = Exports.objects.all()[0]
-        csvdf = pd.read_csv(task.filename.path)
-
-        cols = [
-            "Institution",
-            "Manufacturer",
-            "Model name",
-            "Station name",
-            "Display name",
-            "Accession number",
-            "Operator",
-            "Study date",
-            "Study time",
-            "Age",
-            "Sex",
-            "Test patient?",
-            "Study description",
-            "Requested procedure",
-            "Study Comments",
-            "No. events",
-            "View",
-            "View Modifier",
-            "Laterality",
-            "Acquisition",
-            "Thickness",
-            "Radiological thickness",
-            "Force",
-            "Mag",
-            "Area",
-            "Mode",
-            "Target",
-            "Filter",
-            "Filter thickness",
-            "Focal spot size",
-            "kVp",
-            "mA",
-            "ms",
-            "uAs",
-            "ESD",
-            "AGD",
-            "% Fibroglandular tissue",
-            "Exposure mode description",
-        ]
-        exportline = [
-            "中心医院",
-            "GE MEDICAL SYSTEMS",
-            "Senograph DS ADS_43.10.1",
-            "SENODS01",
-            "中心医院 SENODS01",
-            "AAAA9876",
-            "",
-            "2013-04-12",
-            "12:35:46",
-            "0.000",
-            "O",
-            "",
-            "",
-            "",
-            "",
-            "1",
-            "cranio-caudal",
-            "",
-            "Left",
-            "ROUTINE",
-            "53.00000000",
-            "45.00000000",
-            "50.00000000",
-            "1.00000000",
-            "0.04373900",
-            "AUTOMATIC",
-            "Rh",
-            "Rh",
-            "",
-            "0.30000000",
-            "29.00000000",
-            "61.00000000",
-            "834.00",
-            "51800.00",
-            "5.07100000",
-            "1.37300000",
-            "31.00000000",
-            "AOP standard RECTANGLE 1662 mm 10 mm 180 mm 240 mm EXP DOSE 87504 nGy PRE-EXP DOSE 5655 nGy "
-            "PRE-EXP THICK 45 mm PRE-EXP COMPO 29 % PRE-EXP KV 28 PRE-EXP TRACK Rh PRE-EXP FILTER Rh PADDLE "
-            "1 FLATFIELD no",
-        ]
-        refdf = pd.DataFrame([exportline], columns=cols, index=list(range(1)))
-
-        self.assertEqual(list(csvdf.columns), cols)
-        for col in cols:
-            if pd.isnull(csvdf[col][0]):  # deals with missing data
-                self.assertEqual("", refdf[col][0])
-            elif type(csvdf[col][0]) is str:  # compare all the string values
-                self.assertEqual(csvdf[col][0], refdf[col][0])
-            else:  # assume all other values are numbers
-                self.assertAlmostEqual(csvdf[col][0], float(refdf[col][0]))
-
-        # cleanup
-        task.filename.delete()  # delete file so local testing doesn't get too messy!
-
-
-class ExportMammoCSVNHSBSP(TestCase):
-    def setUp(self):
-        self.factory = RequestFactory()
-        self.user = User.objects.create_user(
-            username="jacob", email="jacob@…", password="top_secret"
-        )
-        eg = Group(name="exportgroup")
-        eg.save()
-        eg.user_set.add(self.user)
-        eg.save()
-
-        PatientIDSettings.objects.create()
-
-        dicom_file = os.path.join("test_files", "MG-RDSR-Hologic_mix.dcm")
-        root_tests = os.path.dirname(os.path.abspath(__file__))
-        dicom_path = os.path.join(root_tests, dicom_file)
-
-        rdsr.rdsr(dicom_path)
-
-    def test_nhsbsp(self):
-        import pandas as pd
-
-        filter_set = {
-            "o": "-projectionxrayradiationdose__accumxraydose__accummammographyxraydose__accumulated_"
-            "average_glandular_dose"
-        }
-
-        mg_csv_nhsbsp(filter_set, user=self.user)
-
-        task = Exports.objects.all()[0]
-        csvdf = pd.read_csv(task.filename.path)
-
-        # Test there are only seven data rows (and fifteen columns), ie no duplication from AGD ordering
-        self.assertEqual(csvdf.shape, (7, 15))
-
-        # Test all three filters are in the results in the right quantities
-        self.assertEqual(
-            Counter(csvdf.Filter.tolist()),
-            Counter(["Al", "Al", "Al", "Al", "Ag", "Rh", "Rh"]),
-        )
-
-        # Test numbered view codes
-        self.assertEqual(
-            Counter(csvdf["View code"].tolist()),
-            Counter(["RCC", "RCC2", "RCC3", "RCC4", "RCC5", "ROB", "LCC"]),
-        )
-
-        # Test each row
-        rcc1 = csvdf[
-            csvdf["View code"].str.contains("RCC")
-            & (csvdf["Filter"] == "Al")
-            & (csvdf["Thickness"] == 19.0)
-        ]
-        self.assertAlmostEqual(rcc1.mAs.values[0], 34.3)
-        self.assertAlmostEqual(rcc1.kV.values[0], 26.0)
-
-        rcc4 = csvdf[
-            csvdf["View code"].str.contains("RCC")
-            & (csvdf["Filter"] == "Al")
-            & (csvdf["Thickness"] == 20.0)
-        ]
-        self.assertAlmostEqual(rcc4.mAs.values[0], 33.9)
-        self.assertAlmostEqual(rcc4.kV.values[0], 26.0)
-
-        rob1 = csvdf[csvdf["View code"].str.contains("ROB")]
-        self.assertAlmostEqual(rob1.mAs.values[0], 35.6)
-        self.assertAlmostEqual(rob1.kV.values[0], 26.0)
-        self.assertEqual(rob1.Filter.values[0], "Al")
-        self.assertAlmostEqual(rob1.Thickness.values[0], 21.0)
-
-        lcc1 = csvdf[csvdf["View code"].str.contains("LCC")]
-        self.assertAlmostEqual(lcc1.mAs.values[0], 33.9)
-        self.assertAlmostEqual(lcc1.kV.values[0], 26.0)
-        self.assertEqual(lcc1.Filter.values[0], "Al")
-        self.assertAlmostEqual(lcc1.Thickness.values[0], 20.0)
-
-        rcc2 = csvdf[
-            csvdf["View code"].str.contains("RCC")
-            & (csvdf["Filter"] == "Rh")
-            & (csvdf["Thickness"] == 23.0)
-        ]
-        self.assertAlmostEqual(rcc2.mAs.values[0], 17.9)
-        self.assertAlmostEqual(rcc2.kV.values[0], 20.0)
-
-        rcc5 = csvdf[
-            csvdf["View code"].str.contains("RCC")
-            & (csvdf["Filter"] == "Rh")
-            & (csvdf["Thickness"] == 46.0)
-        ]
-        self.assertAlmostEqual(rcc5.mAs.values[0], 17.8)
-        self.assertAlmostEqual(rcc5.kV.values[0], 20.0)
-
-        rcc3 = csvdf[csvdf["View code"].str.contains("RCC") & (csvdf["Filter"] == "Ag")]
-        self.assertAlmostEqual(rcc3.mAs.values[0], 17.9)
-        self.assertAlmostEqual(rcc3.kV.values[0], 20.0)
-        self.assertAlmostEqual(rcc3.Thickness.values[0], 128.0)
-
-        # cleanup
-        task.filename.delete()  # delete file so local testing doesn't get too messy!
+# This Python file uses the following encoding: utf-8
+# test_export_mammo_csv.py
+
+from builtins import range  # pylint: disable=redefined-builtin
+import os
+from collections import Counter
+from django.contrib.auth.models import User, Group
+from django.test import TestCase, RequestFactory
+from remapp.extractors import mam, rdsr
+from remapp.exports.mg_export import exportMG2csv
+from remapp.exports.mg_csv_nhsbsp import mg_csv_nhsbsp
+from remapp.models import PatientIDSettings, Exports
+
+
+class ExportMammoCSV(TestCase):
+    def setUp(self):
+        self.factory = RequestFactory()
+        self.user = User.objects.create_user(
+            username="jacob", email="jacob@…", password="top_secret"
+        )
+        eg = Group(name="exportgroup")
+        eg.save()
+        eg.user_set.add(self.user)
+        eg.save()
+
+        PatientIDSettings.objects.create()
+
+        dicom_file = os.path.join("test_files", "MG-Im-GE-SenDS-scaled.dcm")
+        root_tests = os.path.dirname(os.path.abspath(__file__))
+        dicom_path = os.path.join(root_tests, dicom_file)
+
+        mam.mam(dicom_path)
+
+    def test_all_values(self):
+        import pandas as pd
+
+        filter_set = {}
+        pid = False
+        name = False
+        patient_id = False
+
+        exportMG2csv(filter_set, pid=pid, name=name, patid=patient_id, user=self.user)
+
+        task = Exports.objects.all()[0]
+        csvdf = pd.read_csv(task.filename.path)
+
+        cols = [
+            "Institution",
+            "Manufacturer",
+            "Model name",
+            "Station name",
+            "Display name",
+            "Accession number",
+            "Operator",
+            "Study date",
+            "Study time",
+            "Age",
+            "Sex",
+            "Test patient?",
+            "Study description",
+            "Requested procedure",
+            "Study Comments",
+            "No. events",
+            "View",
+            "View Modifier",
+            "Laterality",
+            "Acquisition",
+            "Thickness",
+            "Radiological thickness",
+            "Force",
+            "Mag",
+            "Area",
+            "Mode",
+            "Target",
+            "Filter",
+            "Filter thickness",
+            "Focal spot size",
+            "kVp",
+            "mA",
+            "ms",
+            "uAs",
+            "ESD",
+            "AGD",
+            "% Fibroglandular tissue",
+            "Exposure mode description",
+        ]
+        exportline = [
+            "中心医院",
+            "GE MEDICAL SYSTEMS",
+            "Senograph DS ADS_43.10.1",
+            "SENODS01",
+            "中心医院 SENODS01",
+            "AAAA9876",
+            "",
+            "2013-04-12",
+            "12:35:46",
+            "0.000",
+            "O",
+            "",
+            "",
+            "",
+            "",
+            "1",
+            "cranio-caudal",
+            "",
+            "Left",
+            "ROUTINE",
+            "53.00000000",
+            "45.00000000",
+            "50.00000000",
+            "1.00000000",
+            "0.04373900",
+            "AUTOMATIC",
+            "Rh",
+            "Rh",
+            "",
+            "0.30000000",
+            "29.00000000",
+            "61.00000000",
+            "834.00",
+            "51800.00",
+            "5.07100000",
+            "1.37300000",
+            "31.00000000",
+            "AOP standard RECTANGLE 1662 mm 10 mm 180 mm 240 mm EXP DOSE 87504 nGy PRE-EXP DOSE 5655 nGy "
+            "PRE-EXP THICK 45 mm PRE-EXP COMPO 29 % PRE-EXP KV 28 PRE-EXP TRACK Rh PRE-EXP FILTER Rh PADDLE "
+            "1 FLATFIELD no",
+        ]
+        refdf = pd.DataFrame([exportline], columns=cols, index=list(range(1)))
+
+        self.assertEqual(list(csvdf.columns), cols)
+        for col in cols:
+            if pd.isnull(csvdf[col][0]):  # deals with missing data
+                self.assertEqual("", refdf[col][0])
+            elif type(csvdf[col][0]) is str:  # compare all the string values
+                self.assertEqual(csvdf[col][0], refdf[col][0])
+            else:  # assume all other values are numbers
+                self.assertAlmostEqual(csvdf[col][0], float(refdf[col][0]))
+
+        # cleanup
+        task.filename.delete()  # delete file so local testing doesn't get too messy!
+
+
+class ExportMammoCSVNHSBSP(TestCase):
+    def setUp(self):
+        self.factory = RequestFactory()
+        self.user = User.objects.create_user(
+            username="jacob", email="jacob@…", password="top_secret"
+        )
+        eg = Group(name="exportgroup")
+        eg.save()
+        eg.user_set.add(self.user)
+        eg.save()
+
+        PatientIDSettings.objects.create()
+
+        dicom_file = os.path.join("test_files", "MG-RDSR-Hologic_mix.dcm")
+        root_tests = os.path.dirname(os.path.abspath(__file__))
+        dicom_path = os.path.join(root_tests, dicom_file)
+
+        rdsr.rdsr(dicom_path)
+
+    def test_nhsbsp(self):
+        import pandas as pd
+
+        filter_set = {
+            "o": "-projectionxrayradiationdose__accumxraydose__accummammographyxraydose__accumulated_"
+            "average_glandular_dose"
+        }
+
+        mg_csv_nhsbsp(filter_set, user=self.user)
+
+        task = Exports.objects.all()[0]
+        csvdf = pd.read_csv(task.filename.path)
+
+        # Test there are only seven data rows (and fifteen columns), ie no duplication from AGD ordering
+        self.assertEqual(csvdf.shape, (7, 15))
+
+        # Test all three filters are in the results in the right quantities
+        self.assertEqual(
+            Counter(csvdf.Filter.tolist()),
+            Counter(["Al", "Al", "Al", "Al", "Ag", "Rh", "Rh"]),
+        )
+
+        # Test numbered view codes
+        self.assertEqual(
+            Counter(csvdf["View code"].tolist()),
+            Counter(["RCC", "RCC2", "RCC3", "RCC4", "RCC5", "ROB", "LCC"]),
+        )
+
+        # Test each row
+        rcc1 = csvdf[
+            csvdf["View code"].str.contains("RCC")
+            & (csvdf["Filter"] == "Al")
+            & (csvdf["Thickness"] == 19.0)
+        ]
+        self.assertAlmostEqual(rcc1.mAs.values[0], 34.3)
+        self.assertAlmostEqual(rcc1.kV.values[0], 26.0)
+
+        rcc4 = csvdf[
+            csvdf["View code"].str.contains("RCC")
+            & (csvdf["Filter"] == "Al")
+            & (csvdf["Thickness"] == 20.0)
+        ]
+        self.assertAlmostEqual(rcc4.mAs.values[0], 33.9)
+        self.assertAlmostEqual(rcc4.kV.values[0], 26.0)
+
+        rob1 = csvdf[csvdf["View code"].str.contains("ROB")]
+        self.assertAlmostEqual(rob1.mAs.values[0], 35.6)
+        self.assertAlmostEqual(rob1.kV.values[0], 26.0)
+        self.assertEqual(rob1.Filter.values[0], "Al")
+        self.assertAlmostEqual(rob1.Thickness.values[0], 21.0)
+
+        lcc1 = csvdf[csvdf["View code"].str.contains("LCC")]
+        self.assertAlmostEqual(lcc1.mAs.values[0], 33.9)
+        self.assertAlmostEqual(lcc1.kV.values[0], 26.0)
+        self.assertEqual(lcc1.Filter.values[0], "Al")
+        self.assertAlmostEqual(lcc1.Thickness.values[0], 20.0)
+
+        rcc2 = csvdf[
+            csvdf["View code"].str.contains("RCC")
+            & (csvdf["Filter"] == "Rh")
+            & (csvdf["Thickness"] == 23.0)
+        ]
+        self.assertAlmostEqual(rcc2.mAs.values[0], 17.9)
+        self.assertAlmostEqual(rcc2.kV.values[0], 20.0)
+
+        rcc5 = csvdf[
+            csvdf["View code"].str.contains("RCC")
+            & (csvdf["Filter"] == "Rh")
+            & (csvdf["Thickness"] == 46.0)
+        ]
+        self.assertAlmostEqual(rcc5.mAs.values[0], 17.8)
+        self.assertAlmostEqual(rcc5.kV.values[0], 20.0)
+
+        rcc3 = csvdf[csvdf["View code"].str.contains("RCC") & (csvdf["Filter"] == "Ag")]
+        self.assertAlmostEqual(rcc3.mAs.values[0], 17.9)
+        self.assertAlmostEqual(rcc3.kV.values[0], 20.0)
+        self.assertAlmostEqual(rcc3.Thickness.values[0], 128.0)
+
+        # cleanup
+        task.filename.delete()  # delete file so local testing doesn't get too messy!