Added diana-cli using Click library

apps/cli.old/README.md

@@ -0,0 +1,94 @@
+DIANA CLI Applications
+================
+
+Derek Merck  
+<derek_merck@brown.edu>  
+Rhode Island Hospital and Brown University  
+Providence, RI  
+
+## `diana-lookup.py`
+
+Wrapper command-line tool for a _Splunk_ query.
+
+```
+> python3 diana-lookup.py --query "index=dose_report" -e "-1d" -l now -i my_splunk -s secrets.yml
+```
+
+`secrets.yml` must have a section called "my_splunk" with keys suitable for creating
+an Splunk instance that can accept the query.
+
+
+## `diana-pull.py`
+
+Wrapper command-line tool for an _Orthanc Proxy_ retrieve from modality.
+
+```
+> python3 pull-it.py -accession XYZ -series "thin * brain -p my_proxy -d my_pacs -s secrets.yml
+```
+
+`secrets.yml` must have a section called "my_proxy" with keys suitable for creating
+an Orthanc instance that knows about the remote "my_pacs".
+
+
+## `diana-star.py`
+
+Wrapper command-line tool to stand up a DIANA distributed worker node for pipeline data processing.
+
+
+## `diana-watcher.py`
+
+Wrapper command-line tool to stand up a DIANA watcher daemon.  Can be configured with environment vars for remote/embedded deployment, a yml/json routing file, or a directory of python routes.
+
+
+## `halibut.py`
+
+Wrapper for Halibut machine learning module (use weights in `tests`).
+
+
+## `dcm2im.py`
+
+Wrapper command-line tool to convert pixels from a DICOM format file or directory
+into a standard image format (png, jpg).
+
+```
+> python dcm2py.py -i im000001.dcm
+```
+
+## `index-it.py`
+
+Wrapper command-line tool for pre-index caching and restoring.
+
+```
+$ python3 index-it.py --location /my_path --redis_service my_redis -s secrets.yml
+
+$ python3 index-it.py -l /my_path -r my_redis -s secrets.yml restore --an abcxyz123 -d orthanc
+```
+
+`secrets.yml` must have a section called "my_redis" with keys suitable for creating
+a Redis instance.
+
+No python3 on a system that needs re-indexed?  Docker to the rescue...
+
+```
+$ docker run -v /orthanc/db:/orthanc/db -it derekmerck/diana /bin/bash
+# scp server:/secrets.yml .
+# python3 apps/cli/index-it.py -l /orthanc/db -r redis -s secrets.yml index -w orthanc
+```
+
+## `monitor-dose.py`
+
+monitor-dose
+Merck, Summer 2018
+
+Wrapper to configure and run a DoseReportHarvester daemon.
+
+```
+$ python3 dose-monitor -q "gepacs" -j "dose_reports"
+```
+
+
+
+License
+-------------
+
+[MIT](http://opensource.org/licenses/mit-license.html)

apps/cli/diana-indexer.py → apps/cli.old/diana-indexer.py

@@ -16,7 +16,7 @@
 
 $ docker run -v /orthanc/db:/orthanc/db -it derekmerck/diana:amd64 /bin/bash
 # scp server:/secrets.yml .
-# python3 apps/cli/index-it.py -l /orthanc/db -r redis -s /secrets.yml index -w orthanc
+# python3 apps/cli.old/index-it.py -l /orthanc/db -r redis -s /secrets.yml index -w orthanc
 ...
 
 """

apps/cli/README.md

@@ -1,94 +1,31 @@
-DIANA CLI Applications
-================
+# DIANA CLI
 
-Derek Merck  
-<derek_merck@brown.edu>  
-Rhode Island Hospital and Brown University  
-Providence, RI  
-
-## `diana-lookup.py`
+Derek Merck
 
-Wrapper command-line tool for a _Splunk_ query.
+## DICOM Analytics and Archive (DIANA)
 
-```
-> python3 diana-lookup.py --query "index=dose_report" -e "-1d" -l now -i my_splunk -s secrets.yml
-```
+1. `diana` -- Pythonic API for DICOM-related systems and data types
+2. `diana-cli` -- CLI wrapper for invoking tasks and daemons
+3. `diana-stack` -- Docker swarm definitions for DICOM-service stacks
+4. `diana-embedded` -- Balena compose definitions and images for embedded DICOM services
+5. `trialist` -- A Flack front end for a diana-stack supporting multiple image registries
+5. `radcatr` -- TCL UI for RADCAT report review
 
-`secrets.yml` must have a section called "my_splunk" with keys suitable for creating
-an Splunk instance that can accept the query.
 
+## The DIANA Command Line
 
-## `diana-pull.py`
+### Proxied Pull by Accession Number
 
-Wrapper command-line tool for an _Orthanc Proxy_ retrieve from modality.
+Batch:
 
-```
-> python3 pull-it.py -accession XYZ -series "thin * brain -p my_proxy -d my_pacs -s secrets.yml
-```
+$ `DIANA pull --accession_number 12345 --anonymize my_orthanc pacs`
 
-`secrets.yml` must have a section called "my_proxy" with keys suitable for creating
-an Orthanc instance that knows about the remote "my_pacs".
+Batch:
 
+$ `DIANA pull --file accesions.txt --anonymize my_orthanc pacs`
 
-## `diana-star.py`
 
-Wrapper command-line tool to stand up a DIANA distributed worker node for pipeline data processing.
+### Mock Scanner Daemon
 
+$ `DIANA mock --rate 10 my_orthanc`
 
-## `diana-watcher.py`
-
-Wrapper command-line tool to stand up a DIANA watcher daemon.  Can be configured with environment vars for remote/embedded deployment, a yml/json routing file, or a directory of python routes.
-
-
-## `halibut.py`
-
-Wrapper for Halibut machine learning module (use weights in `tests`).
-
-
-## `dcm2im.py`
-
-Wrapper command-line tool to convert pixels from a DICOM format file or directory
-into a standard image format (png, jpg).
-
-```
-> python dcm2py.py -i im000001.dcm
-```
-
-## `index-it.py`
-
-Wrapper command-line tool for pre-index caching and restoring.
-
-```
-$ python3 index-it.py --location /my_path --redis_service my_redis -s secrets.yml
-
-$ python3 index-it.py -l /my_path -r my_redis -s secrets.yml restore --an abcxyz123 -d orthanc
-```
-
-`secrets.yml` must have a section called "my_redis" with keys suitable for creating
-a Redis instance.
-
-No python3 on a system that needs re-indexed?  Docker to the rescue...
-
-```
-$ docker run -v /orthanc/db:/orthanc/db -it derekmerck/diana /bin/bash
-# scp server:/secrets.yml .
-# python3 apps/cli/index-it.py -l /orthanc/db -r redis -s secrets.yml index -w orthanc
-```
-
-## `monitor-dose.py`
-
-monitor-dose
-Merck, Summer 2018
-
-Wrapper to configure and run a DoseReportHarvester daemon.
-
-```
-$ python3 dose-monitor -q "gepacs" -j "dose_reports"
-```
-
-
-
-License
--------------
-
-[MIT](http://opensource.org/licenses/mit-license.html)

apps/cli/commands/hello.py

@@ -0,0 +1,12 @@
+import click
+
+
+@click.command()
+@click.option('--count', default=1, help='Number of greetings.')
+@click.option('--name', prompt='Your name', help='The person to greet.')
+def hello(count, name):
+    """Greets NAME for a total of COUNT times."""
+    click.echo(hello.__doc__)
+
+    for x in range(count):
+        click.echo('Hello %s!' % name)

apps/cli/commands/mock.py

@@ -0,0 +1,58 @@
+import random, logging, time
+from datetime import datetime
+import click
+import attr
+from diana.apis import Orthanc
+from diana.mock import MockStudy
+
+@attr.s
+class MockScanner(object):
+    seed = attr.ib( default=None )
+    name = attr.ib( type=str, default="Mock Scanner" )
+    modality = attr.ib( type=str, default="CT" )
+    rate = attr.ib( type=float, default=10, converter=float )
+
+    @seed.validator
+    def set_seed(self, attribute, value):
+        if value:
+            random.seed(value)
+
+    def gen_study(self):
+        s = MockStudy(seed=self.seed,
+                      study_datetime=datetime.now(),
+                      station_name = self.name,
+                      modality=self.modality )
+        return s
+
+    def run(self, dest: Orthanc):
+
+        while True:
+
+            logging.info("Generating mock study")
+            s = self.gen_study()
+
+            for d in s.dixels():
+                # logging.debug(d)
+                d.gen_file()
+                dest.put( d )
+
+            ave_delay  = 60*60/self.rate
+            this_delay = random.gauss(ave_delay, ave_delay*0.3)
+            if this_delay < 0.1:
+                this_delay = 0.1
+            logging.info("Waiting {} secs".format(this_delay))
+            time.sleep( this_delay )
+
+
+@click.command()
+@click.argument('destination')
+@click.argument('rate')
+@click.pass_context
+def mock(ctx, destination, rate):
+    """Generate mock studies at RATE per hour and submit to DESTINATION"""
+    click.echo(mock.__doc__)
+    services = ctx.obj['SERVICES']
+
+    D = Orthanc(**services.get(destination))
+    M = MockScanner(name = "Diana Mock", rate = rate)
+    M.run(dest=D)

apps/cli/commands/orthanc.py

@@ -0,0 +1,97 @@
+import logging
+from hashlib import md5
+import click
+import yaml
+from diana.apis import Orthanc, DicomFile
+from diana.utils.dicom import DicomLevel
+
+
+# TODO: Query should always include StudyDate, StudyTime, AccessionNumber
+# Without StudyDate/StudyTime it fails on readback
+
+@click.command()
+@click.argument('query')
+@click.argument('source')
+@click.option('--domain', help="Domain for proxied query")
+@click.option('-r', '--retrieve', default=False)
+@click.pass_context
+def ofind(ctx, query, source, domain, retrieve):
+    """Find items matching json QUERY in SOURCE Orthanc service {optionally with proxy DOMAIN}"""
+    click.echo(ofind.__doc__)
+    services = ctx.obj['SERVICES']
+
+    S = Orthanc(**services.get(source))
+    if isinstance(query, str):
+        query = yaml.safe_load(query)
+    click.echo(S.find(query, DicomLevel.STUDIES, domain, retrieve=retrieve))
+
+
+@click.command()
+@click.option("--accession_number", required=False)
+@click.option("--worklist", type=click.File(), required=False)
+@click.argument('source')
+@click.argument('domain')
+@click.argument('destination', type=click.Path(), required=False)
+@click.option('-a', '--anonymize', default=False, is_flag=True)
+@click.pass_context
+def pull(ctx, accession_number, worklist, source, domain, destination, anonymize):
+    """Pull items matching QUERY from SOURCE Orthanc service with proxy DOMAIN"""
+    click.echo(pull.__doc__)
+    services = ctx.obj['SERVICES']
+
+    S = Orthanc(**services.get(source))
+    # ep.clear()
+    click.echo(S)
+
+    D = None
+    if destination:
+        D = DicomFile(location=destination)
+
+    def get_by_accession_num(accession_num):
+
+        # Only if it's a file destination...
+        if destination:
+            # If dest is DicomFile
+            if D.check("{}.zip".format(md5(accession_num.encode('UTF8')).hexdigest())):
+                click.echo("Skipping {}".format(accession_num))
+                return
+
+        q = {
+             "AccessionNumber": accession_num,
+             "StudyDate": "",
+             "StudyTime": "",
+             "PatientName": "",
+             "PatientBirthDate": "",
+             "PatientSex": ""
+             }
+        dixels = S.find(q, DicomLevel.STUDIES, domain, retrieve=True)
+        click.echo(dixels)
+
+        for dixel in dixels:
+            if anonymize:
+                dixel = S.anonymize(dixel, remove=True)
+                click.echo(dixel)
+
+            if destination:
+                # If dest is DicomFile
+                dixel = S.get(dixel, view='archive')
+                logging.debug(dixel.meta['AccessionNumber'])
+                D.put(dixel, fn_from="AccessionNumber")
+                S.remove(dixel)
+
+                # If dest is peer or modality node
+                # ep.send(dixel, peer_dest=destination)
+                # ep.remove(dixel)
+
+    if not worklist and not accession_number:
+        logging.warning("No --accession_number or --worklist option provided. Nothing to do.")
+
+    if accession_number:
+        get_by_accession_num(accession_number)
+        return
+
+    if worklist:
+        for accession_num in worklist.readlines():
+            # Get rid of trailing return
+            get_by_accession_num(accession_num.rstrip())
+