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

openrem/remapp/tools/populate_summary.py

@@ -1,193 +1,185 @@
-# This Python file uses the following encoding: utf-8
-#    OpenREM - Radiation Exposure Monitoring tools for the physicist
-#    Copyright (C) 2012-2019  The Royal Marsden NHS Foundation Trust
-#
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    Additional permission under section 7 of GPLv3:
-#    You shall not make any use of the name of The Royal Marsden NHS
-#    Foundation trust in connection with this Program in any press or
-#    other public announcement without the prior written consent of
-#    The Royal Marsden NHS Foundation Trust.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-"""
-..  module:: populate_summary.
-    :synopsis: Populates new summary study-level fields on upgrade to 0.10.
-
-..  moduleauthor:: Ed McDonagh
-
-"""
-
-from django.core.exceptions import ObjectDoesNotExist
-import logging
-from remapp.models import GeneralStudyModuleAttr, SummaryFields
-
-logger = logging.getLogger(__name__)
-
-
-def populate_summary_study_level(modality, study_pk):
-    """Enables the summary level data to be sent as a task at study level
-
-    :param modality: Modality type
-    :param study_pk: GeneralStudyModuleAttr database object primary key
-    :return:
-    """
-    from remapp.extractors.extract_common import (
-        populate_mammo_agd_summary,
-        populate_dx_rf_summary,
-        populate_rf_delta_weeks_summary,
-        ct_event_type_count,
-    )
-
-    try:
-        study = GeneralStudyModuleAttr.objects.get(pk__exact=study_pk)
-    except ObjectDoesNotExist:
-        logger.error(
-            f"Attempt to get {modality} study with pk {study_pk} failed - presumably deleted?"
-        )
-        return
-    try:
-        if modality in ["DX", "RF"]:
-            study.number_of_events = (
-                study.projectionxrayradiationdose_set.get().irradeventxraydata_set.count()
-            )
-            study.save()
-            populate_dx_rf_summary(study)
-            if modality in "RF":
-                populate_rf_delta_weeks_summary(study)
-        elif "MG" in modality:
-            study.number_of_events = (
-                study.projectionxrayradiationdose_set.get().irradeventxraydata_set.count()
-            )
-            study.save()
-            populate_mammo_agd_summary(study)
-        elif modality in "CT":
-            study.number_of_events = (
-                study.ctradiationdose_set.get().ctirradiationeventdata_set.count()
-            )
-            study.total_dlp = (
-                study.ctradiationdose_set.get()
-                .ctaccumulateddosedata_set.get()
-                .ct_dose_length_product_total
-            )
-            study.save()
-            ct_event_type_count(study)
-    except ObjectDoesNotExist:
-        logger.warning(
-            "{0} {1} with study UID {2}: unable to set summary data.".format(
-                study.modality_type, study.pk, study.study_instance_uid
-            )
-        )
-
-
-def populate_summary_ct():
-    """Populate the CT summary fields in GeneralStudyModuleAttr table for existing studies
-
-    :return:
-    """
-
-    try:
-        task = SummaryFields.objects.get(modality_type__exact="CT")
-    except ObjectDoesNotExist:
-        task = SummaryFields.objects.create(modality_type__exact="CT")
-    all_ct = GeneralStudyModuleAttr.objects.filter(modality_type__exact="CT").order_by(
-        "pk"
-    )
-    task.total_studies = all_ct.count()
-    to_process_ct = all_ct.filter(number_of_const_angle__isnull=True)
-    task.current_study = task.total_studies - to_process_ct.count()
-    task.save()
-    logger.debug("Starting migration of CT to summary fields")
-    for study in to_process_ct:
-        populate_summary_study_level("CT", study.pk)
-        task.current_study += 1
-        task.save()
-
-
-def populate_summary_mg():
-    """Populate the MG summary fields in GeneralStudyModuleAttr table for existing studies
-
-    :return:
-    """
-
-    try:
-        task = SummaryFields.objects.get(modality_type__exact="MG")
-    except ObjectDoesNotExist:
-        task = SummaryFields.objects.create(modality_type="MG")
-    all_mg = GeneralStudyModuleAttr.objects.filter(modality_type__exact="MG").order_by(
-        "pk"
-    )
-    task.total_studies = all_mg.count()
-    to_process_mg = (
-        all_mg.filter(total_agd_right__isnull=True)
-        .filter(total_agd_left__isnull=True)
-        .filter(total_agd_both__isnull=True)
-    )
-    task.current_study = task.total_studies - to_process_mg.count()
-    task.save()
-    logger.debug("Starting migration of MG to summary fields")
-    for study in to_process_mg:
-        populate_summary_study_level("MG", study.pk)
-        task.save()
-
-
-def populate_summary_dx():
-    """Populate the DX summary fields in GeneralStudyModuleAttr table for existing studies
-
-    :return:
-    """
-    from django.db.models import Q
-
-    try:
-        task = SummaryFields.objects.get(modality_type__exact="DX")
-    except ObjectDoesNotExist:
-        task = SummaryFields.objects.create(modality_type="DX")
-    all_dx = GeneralStudyModuleAttr.objects.filter(
-        Q(modality_type__exact="DX")
-        | Q(modality_type__exact="CR")
-        | Q(modality_type__exact="PX")
-    ).order_by("pk")
-    task.total_studies = all_dx.count()
-    to_process_dx = all_dx.filter(number_of_events_a__isnull=True)
-    task.current_study = task.total_studies - to_process_dx.count()
-    task.save()
-    logger.debug("Starting migration of DX to summary fields")
-    for study in to_process_dx:
-        populate_summary_study_level("DX", study.pk)
-        task.current_study += 1
-        task.save()
-
-
-def populate_summary_rf():
-    """Populate the RF summary fields in GeneralStudyModuleAttr table for existing studies
-
-    :return:
-    """
-
-    try:
-        task = SummaryFields.objects.get(modality_type__exact="RF")
-    except ObjectDoesNotExist:
-        task = SummaryFields.objects.create(modality_type="RF")
-    all_rf = GeneralStudyModuleAttr.objects.filter(modality_type__exact="RF").order_by(
-        "pk"
-    )
-    task.total_studies = all_rf.count()
-    to_process_rf = all_rf.filter(number_of_events_a__isnull=True)
-    task.current_study = task.total_studies - to_process_rf.count()
-    task.save()
-    logger.debug("Starting migration of RF to summary fields")
-    for study in to_process_rf:
-        populate_summary_study_level("RF", study.pk)
-        task.current_study += 1
-        task.save()
+# This Python file uses the following encoding: utf-8
+#    OpenREM - Radiation Exposure Monitoring tools for the physicist
+#    Copyright (C) 2012-2019  The Royal Marsden NHS Foundation Trust
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    Additional permission under section 7 of GPLv3:
+#    You shall not make any use of the name of The Royal Marsden NHS
+#    Foundation trust in connection with this Program in any press or
+#    other public announcement without the prior written consent of
+#    The Royal Marsden NHS Foundation Trust.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+..  module:: populate_summary.
+    :synopsis: Populates new summary study-level fields on upgrade to 0.10.
+
+..  moduleauthor:: Ed McDonagh
+
+"""
+
+from django.core.exceptions import ObjectDoesNotExist
+import logging
+from remapp.models import GeneralStudyModuleAttr, SummaryFields
+
+logger = logging.getLogger(__name__)
+
+
+def populate_summary_study_level(modality, study_pk):
+    """Enables the summary level data to be sent as a task at study level
+
+    :param modality: Modality type
+    :param study_pk: GeneralStudyModuleAttr database object primary key
+    :return:
+    """
+    from remapp.extractors.extract_common import (
+        populate_mammo_agd_summary,
+        populate_dx_rf_summary,
+        populate_rf_delta_weeks_summary,
+        ct_event_type_count,
+    )
+
+    try:
+        study = GeneralStudyModuleAttr.objects.get(pk=study_pk)
+    except ObjectDoesNotExist:
+        logger.error(
+            f"Attempt to get {modality} study with pk {study_pk} failed - presumably deleted?"
+        )
+        return
+    try:
+        if modality in ["DX", "RF"]:
+            study.number_of_events = (
+                study.projectionxrayradiationdose_set.get().irradeventxraydata_set.count()
+            )
+            study.save()
+            populate_dx_rf_summary(study)
+            if modality in "RF":
+                populate_rf_delta_weeks_summary(study)
+        elif "MG" in modality:
+            study.number_of_events = (
+                study.projectionxrayradiationdose_set.get().irradeventxraydata_set.count()
+            )
+            study.save()
+            populate_mammo_agd_summary(study)
+        elif modality in "CT":
+            study.number_of_events = (
+                study.ctradiationdose_set.get().ctirradiationeventdata_set.count()
+            )
+            study.total_dlp = (
+                study.ctradiationdose_set.get()
+                .ctaccumulateddosedata_set.get()
+                .ct_dose_length_product_total
+            )
+            study.save()
+            ct_event_type_count(study)
+    except ObjectDoesNotExist:
+        logger.warning(
+            "{0} {1} with study UID {2}: unable to set summary data.".format(
+                study.modality_type, study.pk, study.study_instance_uid
+            )
+        )
+
+
+def populate_summary_ct():
+    """Populate the CT summary fields in GeneralStudyModuleAttr table for existing studies
+
+    :return:
+    """
+
+    try:
+        task = SummaryFields.objects.get(modality_type="CT")
+    except ObjectDoesNotExist:
+        task = SummaryFields.objects.create(modality_type="CT")
+    all_ct = GeneralStudyModuleAttr.objects.filter(modality_type="CT").order_by("pk")
+    task.total_studies = all_ct.count()
+    to_process_ct = all_ct.filter(number_of_const_angle__isnull=True)
+    task.current_study = task.total_studies - to_process_ct.count()
+    task.save()
+    logger.debug("Starting migration of CT to summary fields")
+    for study in to_process_ct:
+        populate_summary_study_level("CT", study.pk)
+        task.current_study += 1
+        task.save()
+
+
+def populate_summary_mg():
+    """Populate the MG summary fields in GeneralStudyModuleAttr table for existing studies
+
+    :return:
+    """
+
+    try:
+        task = SummaryFields.objects.get(modality_type="MG")
+    except ObjectDoesNotExist:
+        task = SummaryFields.objects.create(modality_type="MG")
+    all_mg = GeneralStudyModuleAttr.objects.filter(modality_type="MG").order_by("pk")
+    task.total_studies = all_mg.count()
+    to_process_mg = (
+        all_mg.filter(total_agd_right__isnull=True)
+        .filter(total_agd_left__isnull=True)
+        .filter(total_agd_both__isnull=True)
+    )
+    task.current_study = task.total_studies - to_process_mg.count()
+    task.save()
+    logger.debug("Starting migration of MG to summary fields")
+    for study in to_process_mg:
+        populate_summary_study_level("MG", study.pk)
+        task.save()
+
+
+def populate_summary_dx():
+    """Populate the DX summary fields in GeneralStudyModuleAttr table for existing studies
+
+    :return:
+    """
+    from django.db.models import Q
+
+    try:
+        task = SummaryFields.objects.get(modality_type="DX")
+    except ObjectDoesNotExist:
+        task = SummaryFields.objects.create(modality_type="DX")
+    all_dx = GeneralStudyModuleAttr.objects.filter(
+        Q(modality_type__in=["DX", "CR", "PX"])
+    ).order_by("pk")
+    task.total_studies = all_dx.count()
+    to_process_dx = all_dx.filter(number_of_events_a__isnull=True)
+    task.current_study = task.total_studies - to_process_dx.count()
+    task.save()
+    logger.debug("Starting migration of DX to summary fields")
+    for study in to_process_dx:
+        populate_summary_study_level("DX", study.pk)
+        task.current_study += 1
+        task.save()
+
+
+def populate_summary_rf():
+    """Populate the RF summary fields in GeneralStudyModuleAttr table for existing studies
+
+    :return:
+    """
+
+    try:
+        task = SummaryFields.objects.get(modality_type="RF")
+    except ObjectDoesNotExist:
+        task = SummaryFields.objects.create(modality_type="RF")
+    all_rf = GeneralStudyModuleAttr.objects.filter(modality_type="RF").order_by("pk")
+    task.total_studies = all_rf.count()
+    to_process_rf = all_rf.filter(number_of_events_a__isnull=True)
+    task.current_study = task.total_studies - to_process_rf.count()
+    task.save()
+    logger.debug("Starting migration of RF to summary fields")
+    for study in to_process_rf:
+        populate_summary_study_level("RF", study.pk)
+        task.current_study += 1
+        task.save()

openrem/remapp/tools/save_skin_map_structure.py

@@ -1,73 +1,73 @@
-# This Python file uses the following encoding: utf-8
-#    OpenREM - Radiation Exposure Monitoring tools for the physicist
-#    Copyright (C) 2012,2013  The Royal Marsden NHS Foundation Trust
-#
-#    This program is free software: you can redistribute it and/or modify
-#    it under the terms of the GNU General Public License as published by
-#    the Free Software Foundation, either version 3 of the License, or
-#    (at your option) any later version.
-#
-#    This program is distributed in the hope that it will be useful,
-#    but WITHOUT ANY WARRANTY; without even the implied warranty of
-#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-#    GNU General Public License for more details.
-#
-#    Additional permission under section 7 of GPLv3:
-#    You shall not make any use of the name of The Royal Marsden NHS
-#    Foundation trust in connection with this Program in any press or
-#    other public announcement without the prior written consent of
-#    The Royal Marsden NHS Foundation Trust.
-#
-#    You should have received a copy of the GNU General Public License
-#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-"""
-..  module:: save_skin_map_structure.
-    :synopsis: Module to save openskin structure
-
-..  moduleauthor:: Ed McDonagh, David Platten, Wens Kong
-
-"""
-import gzip
-import os
-import pickle
-
-from django.conf import settings
-
-from remapp.models import HighDoseMetricAlertSettings
-from .send_high_dose_alert_emails import send_rf_high_dose_alert_email
-
-
-def save_openskin_structure(study, return_struct):
-    # Save the return_structure as a pickle in a skin_maps sub-folder of the MEDIA_ROOT folder
-    if study:
-        study_date = study.study_date
-        if study_date:
-            skin_map_path = os.path.join(
-                settings.MEDIA_ROOT,
-                "skin_maps",
-                f"{study_date.year:0>4}",
-                f"{study_date.month:0>2}",
-                f"{study_date.day:0>2}",
-            )
-        else:
-            skin_map_path = os.path.join(settings.MEDIA_ROOT, "skin_maps")
-
-        if not os.path.exists(skin_map_path):
-            os.makedirs(skin_map_path)
-
-        with gzip.open(
-            os.path.join(skin_map_path, "skin_map_" + str(study.pk) + ".p"), "wb"
-        ) as pickle_file:
-            pickle.dump(return_struct, pickle_file)
-
-        # send alert email if option toggled on
-        HighDoseMetricAlertSettings.objects.get()
-        send_alert_emails_skin = HighDoseMetricAlertSettings.objects.values_list(
-            "send_high_dose_metric_alert_emails_skin", flat=True
-        )[0]
-        send_alert_emails_ref = HighDoseMetricAlertSettings.objects.values_list(
-            "send_high_dose_metric_alert_emails_ref", flat=True
-        )[0]
-        if send_alert_emails_skin or send_alert_emails_ref:
-            send_rf_high_dose_alert_email(study.pk)
+# This Python file uses the following encoding: utf-8
+#    OpenREM - Radiation Exposure Monitoring tools for the physicist
+#    Copyright (C) 2012,2013  The Royal Marsden NHS Foundation Trust
+#
+#    This program is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    Additional permission under section 7 of GPLv3:
+#    You shall not make any use of the name of The Royal Marsden NHS
+#    Foundation trust in connection with this Program in any press or
+#    other public announcement without the prior written consent of
+#    The Royal Marsden NHS Foundation Trust.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+..  module:: save_skin_map_structure.
+    :synopsis: Module to save openskin structure
+
+..  moduleauthor:: Ed McDonagh, David Platten, Wens Kong
+
+"""
+import gzip
+import os
+import pickle
+
+from django.conf import settings
+
+from remapp.models import HighDoseMetricAlertSettings
+from .send_high_dose_alert_emails import send_rf_high_dose_alert_email
+
+
+def save_openskin_structure(study, return_struct):
+    # Save the return_structure as a pickle in a skin_maps sub-folder of the MEDIA_ROOT folder
+    if study:
+        study_date = study.study_date
+        if study_date:
+            skin_map_path = os.path.join(
+                settings.MEDIA_ROOT,
+                "skin_maps",
+                f"{study_date.year:0>4}",
+                f"{study_date.month:0>2}",
+                f"{study_date.day:0>2}",
+            )
+        else:
+            skin_map_path = os.path.join(settings.MEDIA_ROOT, "skin_maps")
+
+        if not os.path.exists(skin_map_path):
+            os.makedirs(skin_map_path)
+
+        with gzip.open(
+            os.path.join(skin_map_path, "skin_map_" + str(study.pk) + ".p"), "wb"
+        ) as pickle_file:
+            pickle.dump(return_struct, pickle_file)
+
+        # send alert email if option toggled on
+        HighDoseMetricAlertSettings.objects.get()
+        send_alert_emails_skin = HighDoseMetricAlertSettings.objects.values_list(
+            "send_high_dose_metric_alert_emails_skin", flat=True
+        )[0]
+        send_alert_emails_ref = HighDoseMetricAlertSettings.objects.values_list(
+            "send_high_dose_metric_alert_emails_ref", flat=True
+        )[0]
+        if send_alert_emails_skin or send_alert_emails_ref:
+            send_rf_high_dose_alert_email(study.pk)