Merge branch 'main' into monitor-ux-improvements

scripts/monitor/rano_monitor/__main__.py

@@ -8,6 +8,8 @@
     STAGES_HELP,
     DSET_LOC_HELP,
     OUT_HELP,
+    REVIEW_COMMAND,
+    REVIEW_CMD_HELP,
 )
 from rano_monitor.dataset_browser import DatasetBrowser
 from rano_monitor.handlers import InvalidHandler
@@ -21,7 +23,7 @@
 app = typer.Typer()
 
 
-def run_dset_app(dset_path, stages_path, output_path):
+def run_dset_app(dset_path, stages_path, output_path, review_cmd):
     report_path = os.path.join(dset_path, "report.yaml")
     dset_data_path = os.path.join(dset_path, "data")
     invalid_path = os.path.join(dset_path, "metadata/.invalid.txt")
@@ -48,6 +50,7 @@ def run_dset_app(dset_path, stages_path, output_path):
         invalid_path,
         invalid_watchdog,
         prompt_watchdog,
+        review_cmd,
     )
 
     observer = Observer()
@@ -60,7 +63,7 @@ def run_dset_app(dset_path, stages_path, output_path):
     observer.stop()
 
 
-def run_tarball_app(tarball_path):
+def run_tarball_app(tarball_path, review_cmd):
     folder_name = f".{os.path.basename(tarball_path).split('.')[0]}"
     contents_path = os.path.join(os.path.dirname(tarball_path), folder_name)
     if not os.path.exists(contents_path):
@@ -72,7 +75,7 @@ def run_tarball_app(tarball_path):
     contents_path = os.path.join(contents_path, "review_cases")
     reviewed_watchdog = TarballReviewedHandler(contents_path, t_app)
 
-    t_app.set_vars(contents_path)
+    t_app.set_vars(contents_path, review_cmd)
 
     observer = Observer()
     observer.schedule(reviewed_watchdog, path=contents_path, recursive=True)
@@ -94,10 +97,13 @@ def main(
         help=DSET_LOC_HELP,
     ),
     output_path: str = Option(None, "-o", "--out", help=OUT_HELP),
+    itksnap_executable: str = Option(
+        REVIEW_COMMAND, "-i", "--itksnap", help=REVIEW_CMD_HELP
+    ),
 ):
     if dataset_uid.endswith(".tar.gz"):
         # TODO: implement tarball_app
-        run_tarball_app(dataset_uid)
+        run_tarball_app(dataset_uid, itksnap_executable)
         return
     elif dataset_uid.isdigit():
         # Only import medperf dependencies if the user intends to use medperf
@@ -115,7 +121,7 @@ def main(
             "Please ensure the passed dataset UID/path is correct"
         )
 
-    run_dset_app(dset_path, stages_path, output_path)
+    run_dset_app(dset_path, stages_path, output_path, itksnap_executable)
 
 
 if __name__ == "__main__":

scripts/monitor/rano_monitor/constants.py

@@ -24,6 +24,7 @@
 REVIEW_FILENAME = "review_cases.tar.gz"
 REVIEWED_FILENAME = "reviewed_cases.tar.gz"
 REVIEW_COMMAND = "itksnap"
+REVIEW_CMD_HELP = f"path or name of the command that launches itksnap. Defaults to '{REVIEW_COMMAND}'"
 MANUAL_REVIEW_STAGE = 5
 DONE_STAGE = 8
 LISTITEM_MAX_LEN = 30

scripts/monitor/rano_monitor/dataset_browser.py

@@ -49,13 +49,15 @@ def set_vars(
         invalid_path,
         invalid_watchdog,
         prompt_watchdog,
+        review_cmd,
     ):
         self.dset_data_path = dset_data_path
         self.stages_path = stages_path
         self.output_path = output_path
         self.invalid_path = invalid_path
         self.invalid_watchdog = invalid_watchdog
         self.prompt_watchdog = prompt_watchdog
+        self.review_cmd = review_cmd
 
     def update_invalid(self, invalid_subjects):
         self.invalid_subjects = invalid_subjects
@@ -107,6 +109,7 @@ def on_mount(self):
         # Set invalid path for subject view
         subject_details = self.query_one("#details", SubjectDetails)
         subject_details.set_invalid_path(self.invalid_path)
+        subject_details.review_cmd = self.review_cmd
 
         # Set dataset path to listview
         listview = self.query_one("#subjects-list", ListView)

scripts/monitor/rano_monitor/tarball_browser.py

@@ -44,8 +44,9 @@ class TarballBrowser(App):
 
     subjects = var([])
 
-    def set_vars(self, contents_path):
+    def set_vars(self, contents_path, review_cmd):
         self.contents_path = contents_path
+        self.review_cmd = review_cmd
         self.subjects_list = self.__get_subjects()
 
     def __get_subjects(self):
@@ -55,7 +56,9 @@ def __get_subjects(self):
         for subject in subjects:
             subject_path = os.path.join(self.contents_path, subject)
             timepoints = os.listdir(subject_path)
-            timepoints = [timepoint for timepoint in timepoints if not timepoint.startswith(".")]
+            timepoints = [
+                timepoint for timepoint in timepoints if not timepoint.startswith(".")
+            ]
             subject_timepoint_list += [(subject, tp) for tp in timepoints]
 
         return subject_timepoint_list
@@ -76,6 +79,7 @@ def compose(self) -> ComposeResult:
                     subject_view = TarballSubjectView()
                     subject_view.subject = f"{id}|{tp}"
                     subject_view.contents_path = self.contents_path
+                    subject_view.review_cmd = self.review_cmd
                     yield subject_view
 
     def on_mount(self):
@@ -84,7 +88,7 @@ def on_mount(self):
     def update_subjects_status(self):
         subject_views = self.query(TarballSubjectView)
         editor_msg = self.query_one("#review-msg", Static)
-        editor_msg.display = "none" if is_editor_installed() else "block"
+        editor_msg.display = "none" if is_editor_installed(self.review_cmd) else "block"
 
         for subject_view in subject_views:
             subject_view.update_status()

scripts/monitor/rano_monitor/utils.py

@@ -9,7 +9,6 @@
 import pandas as pd
 import yaml
 from rano_monitor.constants import (
-    REVIEW_COMMAND,
     BRAINMASK_BAK,
     DEFAULT_SEGMENTATION,
     BRAINMASK,
@@ -22,8 +21,8 @@
 )
 
 
-def is_editor_installed():
-    review_command_path = shutil.which(REVIEW_COMMAND)
+def is_editor_installed(review_command):
+    review_command_path = shutil.which(review_command)
     return review_command_path is not None
 
 
@@ -34,10 +33,10 @@ def get_hash(filepath: str):
     return file_hash
 
 
-def run_editor(t1c, flair, t2, t1, seg, label, cmd=REVIEW_COMMAND):
+def run_editor(t1c, flair, t2, t1, seg, label, cmd):
     review_cmd = "{cmd} -g {t1c} -o {flair} {t2} {t1} -s {seg} -l {label}"
     review_cmd = review_cmd.format(
-        cmd=REVIEW_COMMAND,
+        cmd=cmd,
         t1c=t1c,
         flair=flair,
         t2=t2,
@@ -48,7 +47,9 @@ def run_editor(t1c, flair, t2, t1, seg, label, cmd=REVIEW_COMMAND):
     Popen(review_cmd.split(), shell=False, stdout=DEVNULL, stderr=DEVNULL)
 
 
-def review_tumor(subject: str, data_path: str, labels_path: str):
+def review_tumor(
+    subject: str, data_path: str, labels_path: str, review_cmd: str
+):
     (
         t1c_file,
         t1n_file,
@@ -65,10 +66,18 @@ def review_tumor(subject: str, data_path: str, labels_path: str):
     if not is_nifti and not is_under_review:
         shutil.copyfile(seg_file, under_review_file)
 
-    run_editor(t1c_file, t2f_file, t2w_file, t1n_file, under_review_file, label_file)
+    run_editor(
+        t1c_file,
+        t2f_file,
+        t2w_file,
+        t1n_file,
+        under_review_file,
+        label_file,
+        cmd=review_cmd,
+    )
 
 
-def review_brain(subject, labels_path, data_path=None):
+def review_brain(subject, labels_path, review_cmd, data_path=None):
     (
         t1c_file,
         t1n_file,
@@ -82,7 +91,9 @@ def review_brain(subject, labels_path, data_path=None):
     if not os.path.exists(backup_path):
         shutil.copyfile(seg_file, backup_path)
 
-    run_editor(t1c_file, t2f_file, t2w_file, t1n_file, seg_file, label_file)
+    run_editor(
+        t1c_file, t2f_file, t2w_file, t1n_file, seg_file, label_file, cmd=review_cmd
+    )
 
 
 def finalize(subject: str, labels_path: str):

scripts/monitor/rano_monitor/widgets/subject_details.py

@@ -25,6 +25,7 @@ class SubjectDetails(Static):
     invalid_subjects = set()
     subject = pd.Series()
     dset_path = ""
+    review_cmd = None  # This will be assigned after initialized
 
     def compose(self) -> ComposeResult:
         with Center(id="subject-title"):
@@ -51,10 +52,7 @@ def compose(self) -> ComposeResult:
                 id="reviewed-button",
                 disabled=True,
             )
-            yield Static(
-                "If brain mask is not correct",
-                id="brianmask-review-header"
-            )
+            yield Static("If brain mask is not correct", id="brianmask-review-header")
             yield Button(
                 "Brain mask not available",
                 disabled=True,
@@ -134,7 +132,7 @@ def __update_buttons(self):
         brainmask_button = self.query_one("#brainmask-review-button", Button)
         valid_btn = self.query_one("#valid-btn", Button)
 
-        if is_editor_installed():
+        if is_editor_installed(self.review_cmd):
             review_msg.display = "none"
             review_button.disabled = False
         if self.__can_finalize():
@@ -175,15 +173,15 @@ def __review_tumor(self):
         data_path = to_local_path(data_path, self.dset_path)
         labels_path = self.subject["labels_path"]
         labels_path = to_local_path(labels_path, self.dset_path)
-        review_tumor(subject, data_path, labels_path)
+        review_tumor(subject, data_path, labels_path, review_cmd=self.review_cmd)
         self.__update_buttons()
         self.notify("This subject can be finalized now")
 
     def __review_brainmask(self):
         subject = self.subject.name
         labels_path = self.subject["labels_path"]
         labels_path = to_local_path(labels_path, self.dset_path)
-        review_brain(subject, labels_path)
+        review_brain(subject, labels_path, review_cmd=self.review_cmd)
         self.__update_buttons()
 
     def __finalize(self):

scripts/monitor/rano_monitor/widgets/tarball_subject_view.py

@@ -18,6 +18,7 @@
 class TarballSubjectView(Static):
     subject = reactive("")
     contents_path = reactive("")
+    review_cmd = None  # This will be assigned after initialized
 
     def compose(self) -> ComposeResult:
         with Horizontal(classes="subject-item"):
@@ -64,7 +65,7 @@ def __update_buttons(self):
         tumor_btn = self.query_one(".tumor-btn", Button)
         finalize_btn = self.query_one(".finalize-btn", Button)
         brain_btn = self.query_one(".brain-btn", Button)
-        if is_editor_installed():
+        if is_editor_installed(self.review_cmd):
             tumor_btn.disabled = False
         if self.__can_finalize():
             finalize_btn.disabled = False
@@ -87,19 +88,19 @@ def __can_review_brain(self):
         id, tp = self.subject.split("|")
         filepath = os.path.join(self.contents_path, id, tp, BRAINMASK)
 
-        return os.path.exists(filepath) and is_editor_installed()
+        return os.path.exists(filepath) and is_editor_installed(self.review_cmd)
 
     def __review_tumor(self):
         id, tp = self.subject.split("|")
         data_path = os.path.join(self.contents_path, id, tp, "brain_scans")
         labels_path = os.path.join(self.contents_path, id, tp)
-        review_tumor(self.subject, data_path, labels_path)
+        review_tumor(self.subject, data_path, labels_path, review_cmd=self.review_cmd)
 
     def __review_brainmask(self):
         id, tp = self.subject.split("|")
         data_path = os.path.join(self.contents_path, id, tp, "raw_scans")
         labels_path = os.path.join(self.contents_path, id, tp)
-        review_brain(self.subject, labels_path, data_path)
+        review_brain(self.subject, labels_path, self.review_cmd, data_path)
 
     def __finalize(self):
         id, tp = self.subject.split("|")
@@ -119,3 +120,23 @@ def on_button_pressed(self, event: Button.Pressed) -> None:
             self.__finalize()
 
         self.__update_buttons()
+
+    def __brain_has_been_reviewed(self):
+        id, tp = self.subject.split("|")
+        brainpath = os.path.join(self.contents_path, id, tp, BRAINMASK)
+        backup_brainpath = os.path.join(self.contents_path, id, tp, BRAINMASK_BAK)
+
+        if not os.path.exists(backup_brainpath):
+            return False
+
+        brain_hash = get_hash(brainpath)
+        backup_hash = get_hash(backup_brainpath)
+        return brain_hash != backup_hash
+
+    def __tumor_has_been_finalized(self):
+        id, tp = self.subject.split("|")
+        finalized_tumor_path = os.path.join(self.contents_path, id, tp, "finalized")
+        finalized_files = os.listdir(finalized_tumor_path)
+        finalized_files = [file for file in finalized_files if not file.startswith(".")]
+
+        return len(finalized_files) > 0