anatools 5.1.28__py3-none-any.whl → 6.0.1__py3-none-any.whl

anatools/anaclient/services.py

@@ -174,15 +174,40 @@ def build_service(self, servicefile):
         disk_usage = shutil.disk_usage('/')
         gb_free = disk_usage.free / (1024**3)  # Convert bytes to GB
         if self.verbose == 'debug': print(f"Disk space left: {gb_free:.3f}GB")
-        if gb_free < 20: print_color(f'\nWarning: Low disk space detected! Only {gb_free:.1f}GB available.', 'ffff00')
+        if gb_free < 20 and self.interactive: print_color(f'\nWarning: Low disk space detected! Only {gb_free:.1f}GB available.', 'ffff00')
         docker_space_cmd = "docker system df --format json"
         result = subprocess.run(docker_space_cmd, shell=True, capture_output=True, text=True)
         if result.returncode == 0:
-            docker_stats = json.loads(result.stdout)
-            total_docker_size = sum(item.get('Size', 0) for item in docker_stats if 'Size' in item)
-            docker_gb = total_docker_size / (1024**3)  # Convert bytes to GB
+            # Parse Docker output which may be NDJSON (newline-delimited) or concatenated JSON objects
+            # Use JSONDecoder.raw_decode() to handle both formats robustly
+            import re
+            def parse_docker_json(data):
+                results = []
+                decoder = json.JSONDecoder()
+                idx = 0
+                data = data.strip()
+                while idx < len(data):
+                    obj, end_idx = decoder.raw_decode(data, idx)
+                    results.append(obj)
+                    idx = end_idx
+                    # Skip any whitespace between objects
+                    while idx < len(data) and data[idx].isspace():
+                        idx += 1
+                return results
+            docker_stats = parse_docker_json(result.stdout)
+            # Parse human-readable size strings (e.g., "85.19GB", "2.087MB", "0B") to GB
+            def parse_size_to_gb(size_str):
+                if not size_str or size_str == '0B':
+                    return 0.0
+                match = re.match(r'^([\d.]+)([KMGT]?B)$', size_str)
+                if not match:
+                    return 0.0
+                value, unit = float(match.group(1)), match.group(2)
+                multipliers = {'B': 1/(1024**3), 'KB': 1/(1024**2), 'MB': 1/1024, 'GB': 1, 'TB': 1024}
+                return value * multipliers.get(unit, 0)
+            docker_gb = sum(parse_size_to_gb(item.get('Size', '0B')) for item in docker_stats)
             if self.verbose == 'debug': print(f"Docker space used: {docker_gb:.3f}GB")
-            if docker_gb > 20:
+            if docker_gb > 20 and self.interactive:
                 print_color(f'\nWarning: Docker is using {docker_gb:.1f}GB of disk space!', 'ffff00')
                 print_color('Consider running "docker system prune -a" to free up space.', 'ffff00')
                 print_color('This will remove:', 'ffff00')
@@ -191,10 +216,11 @@ def build_service(self, servicefile):
                 print_color('  - All dangling images', 'ffff00')
                 print_color('  - All dangling build cache', 'ffff00')
     except Exception as e:
+        if self.verbose == 'debug': print(f"Docker space check failed: {e}")
         pass
 
     # check for service Dockerfile
-    print('Building Service Image...', end='', flush=True)    
+    if self.interactive: print('Building Service Image...', end='', flush=True)    
     if not os.path.isfile(servicefile): raise Exception(f'No service file {servicefile} found.')
     servicedir, servicefile = os.path.split(servicefile)
     imgtime = int(time.time())
@@ -207,12 +233,12 @@ def build_service(self, servicefile):
     try:
         start = time.time()
         streamer = dockerclient.build(
-            path=servicedir, 
-            dockerfile=os.path.join(servicedir, '.devcontainer/Dockerfile'), 
-            tag=image, 
-            rm=True, 
-            decode=True, 
-            platform='linux/amd64', 
+            path=servicedir,
+            dockerfile=os.path.join(servicedir, '.devcontainer/Dockerfile'),
+            tag=image,
+            rm=True,
+            decode=True,
+            platform='linux/amd64',
             nocache=False,
             pull=False)
         logfilepath = os.path.join(tempfile.gettempdir(), 'dockerbuild.log')
@@ -225,7 +251,7 @@ def build_service(self, servicefile):
                     if 'error' in output: print_color(f'{output["error"]}', 'ff0000')
                 if 'stream' in output: logfile.write(output['stream'])
                 if 'error' in output: logfile.write(output["error"])
-                print(f'\rBuilding Service Image...  [{time.time()-start:.3f}s]', end='', flush=True)
+                if self.interactive: print(f'\rBuilding Service Image...  [{time.time()-start:.3f}s]', end='', flush=True)
             except StopIteration:
                 time.sleep(1)
                 try:
@@ -238,7 +264,7 @@ def build_service(self, servicefile):
         logfile.close()
         raise Exception(f'Error encountered while building Docker image. Please check logfile {logfilepath}.')
     if self.verbose != 'debug' and os.path.exists(logfilepath): os.remove(logfilepath)
-    print(f"\rBuilding Service Image...done.  [{time.time()-start:.3f}s]", flush=True)
+    if self.interactive: print(f"\rBuilding Service Image...done.  [{time.time()-start:.3f}s]", flush=True)
     return image
 
 
@@ -296,13 +322,13 @@ def deploy_service(self, serviceId=None, servicefile=None):
                 progressDetail = line['progressDetail']
                 if progressDetail['total'] >= largest:
                     largest = progressDetail['total']
-                    print(f"\rPushing Service Image...  [{time.time()-start:.3f}s, {min(100,round((progressDetail['current']/progressDetail['total']) * 100))}%]", end='', flush=True)
-        if 'error' in line: 
+                    if self.interactive: print(f"\rPushing Service Image...  [{time.time()-start:.3f}s, {min(100,round((progressDetail['current']/progressDetail['total']) * 100))}%]", end='', flush=True)
+        if 'error' in line:
             if 'HTTP 403' in line['error']: raise Exception('You do not have permission to push to this repository.')
             else: raise Exception(line['error'])
     logfile.close()
     if self.verbose != 'debug' and os.path.exists(logfilepath): os.remove(logfilepath)
-    print(f"\rPushing Service Image...done.  [{time.time()-start:.3f}s]     ", flush=True)
+    if self.interactive: print(f"\rPushing Service Image...done.  [{time.time()-start:.3f}s]     ", flush=True)
     
     # cleanup docker and update services
     dockerclient.images.remove(reponame)
@@ -331,13 +357,13 @@ def get_service_deployment(self, deploymentId, stream=False):
     if deploymentId is None: raise Exception('DeploymentId must be specified.')
     if stream:
         data = self.ana_api.getServiceDeployment(deploymentId=deploymentId)
-        print(f"\r\tStep {data['status']['step']} - {data['status']['message']}", end='', flush=True)
+        if self.interactive: print(f"\r\tStep {data['status']['step']} - {data['status']['message']}", end='', flush=True)
         while (data['status']['state'] not in ['Service Deployment Complete','Service Deployment Failed']):
             time.sleep(10)
-            print(f"\r\tStep {data['status']['step']} - {data['status']['message']}", end='', flush=True)
+            if self.interactive: print(f"\r\tStep {data['status']['step']} - {data['status']['message']}", end='', flush=True)
             if self.check_logout(): return
             data = self.ana_api.getServiceDeployment(deploymentId=deploymentId)
-        print(f"\r\tStep {data['status']['step']} - {data['status']['message']}", flush=True)
+        if self.interactive: print(f"\r\tStep {data['status']['step']} - {data['status']['message']}", flush=True)
         return data
     else: return self.ana_api.getServiceDeployment(deploymentId=deploymentId)
 

anatools/anaclient/volumes.py

@@ -274,8 +274,8 @@ def download_volume_data(self, volumeId, files=[], localDir=None, recursive=True
                 if self.interactive: 
                     print(f"\x1b[1K\rdownload: {response[index]['key']} to {filename}", flush=True)
             except:
-                traceback.print_exc()
-                print(f"\x1b[1K\rdownload: failed to download {response[index]['key']}", flush=True)
+                if self.verbose: traceback.print_exc()
+                if self.interactive: print(f"\x1b[1K\rdownload: failed to download {response[index]['key']}", flush=True)
     return
 
 
@@ -330,7 +330,8 @@ def upload_volume_data(self, volumeId, files=None, localDir=None, destinationDir
                 if sync == True:
                     file_hash = generate_etag(filepath)
                     source_hashes.append(file + file_hash)
-            else: print(f"Could not find {filepath}.")
+            else:
+                if self.interactive: print(f"Could not find {filepath}.")
     else:
         for root, dirs, files in os.walk(localDir):
             for file in files:
@@ -371,37 +372,37 @@ def upload_volume_data(self, volumeId, files=None, localDir=None, destinationDir
                 delete_files.append(destination_file)  
 
         if (len(delete_files)):
-            print(f"The following files will be deleted:", end='\n', flush=True)
-            for file in delete_files:
-                print(f"   {file}", end='\n', flush=True)
-            answer = input("Delete these files [Y/n]: ")
-            if answer.lower() == "y":
-                self.refresh_token()
-                self.ana_api.deleteVolumeData(volumeId=volumeId, keys=delete_files)
+            if self.interactive:
+                print(f"The following files will be deleted:", end='\n', flush=True)
+                for file in delete_files:
+                    print(f"   {file}", end='\n', flush=True)
+                answer = input("Delete these files [Y/n]: ")
+                if answer.lower() == "y":
+                    self.refresh_token()
+                    self.ana_api.deleteVolumeData(volumeId=volumeId, keys=delete_files)
 
     for index, file in enumerate(source_files):
         destination_key = (destinationDir or '') + file
-        print(f"\x1b[1K\rUploading {file} to the volume [{index+1} / {len(source_files)}]", end='\n' if self.verbose else '', flush=True)
+        if self.interactive: print(f"\x1b[1K\rUploading {file} to the volume [{index+1} / {len(source_files)}]", end='\n' if self.verbose else '', flush=True)
         if (sync == True and (source_hashes[index] in destination_hashes)):
-            print(f"\x1b[1K\rsync: {file}'s hash exists", end='\n' if self.verbose else '', flush=True)
+            if self.interactive: print(f"\x1b[1K\rsync: {file}'s hash exists", end='\n' if self.verbose else '', flush=True)
         elif sync == False or (source_hashes[index] not in destination_hashes):
             try:
                 self.refresh_token()
                 filepath = os.path.join(localDir, file)
                 filesize = os.path.getsize(filepath)
                 fileinfo = self.ana_api.uploadVolumeData(volumeId=volumeId, key=destination_key, size=filesize)
-                # print(f"\x1b[1K\rupload: {file} to the volume. [{index+1} / {len(source_files)}]", end='\n' if self.verbose else '', flush=True)
-                parts = multipart_upload_file(filepath, int(fileinfo["partSize"]), fileinfo["urls"], f"Uploading {file} to the volume [{index+1} / {len(source_files)}]")
+                parts = multipart_upload_file(filepath, int(fileinfo["partSize"]), fileinfo["urls"], f"Uploading {file} to the volume [{index+1} / {len(source_files)}]", interactive=self.interactive)
                 self.refresh_token()
                 finalize_success = self.ana_api.uploadVolumeDataFinalizer(uploadId=fileinfo['uploadId'], key=fileinfo['key'], parts=parts)
                 if not finalize_success:
                     faileduploads.append(file)
             except:
-                traceback.print_exc()
+                if self.verbose: traceback.print_exc()
                 faileduploads.append(file)
-                print(f"\x1b[1K\rupload: {file} failed", end='\n' if self.verbose else '', flush=True)
-    print("\x1b[1K\rUploading files completed.", flush=True)
-    if len(faileduploads): print('The following files failed to upload:', faileduploads, flush=True)
+                if self.interactive: print(f"\x1b[1K\rupload: {file} failed", end='\n' if self.verbose else '', flush=True)
+    if self.interactive: print("\x1b[1K\rUploading files completed.", flush=True)
+    if len(faileduploads) and self.interactive: print('The following files failed to upload:', faileduploads, flush=True)
     return
             
 

anatools/annotations/annotations.py

@@ -14,15 +14,15 @@ class annotations:
     Examples of mapfiles are in the example channel at /ana/channels/example/mapfiles/.
     """
 
-    def bounding_box_2d(self, image_path, out_dir, object_ids=None, object_types=None, line_thickness=1, colors=None):
+    def bounding_box_2d(self, image_path, out_dir, object_ids=None, object_types=None, line_thickness=1, colors=None, quiet=False):
         """
-        Generates images annotated with 2d bounding boxes for datasets downloaded from the Platform. Optional filter on 
+        Generates images annotated with 2d bounding boxes for datasets downloaded from the Platform. Optional filter on
         object_ids or object_types (must choose a single filter).
-        
+
         Parameters
         ----------
         image_path : str
-            Path to of specific image file to draw the boxes for.  
+            Path to of specific image file to draw the boxes for.
         out_dir : str
             File path to directory where the image should be saved to.
         object_ids : list[int]
@@ -30,22 +30,29 @@ class annotations:
         object_types: list[str]
             Filter for the object types to annotate. If not provided, all object types will get annotated. Choose either id or type filter.
         line_thickness: int
-            Desired line thickness for box outline. 
-         colors: dict
+            Desired line thickness for box outline.
+        colors: dict
             Dictionary of colors to use for each object type where each color is a tuple of 3 integers (R, G, B). For example: colors={'Car': (255, 0, 0)}
+        quiet: bool
+            If True, suppress print output. Useful for CLI/automation.
+
+        Returns
+        -------
+        str or None
+            Path to the saved annotated image, or None if an error occurred.
         """
-        draw(image_path, out_dir, draw_type='box_2d', object_ids=object_ids, object_types=object_types, line_thickness=line_thickness, colors=colors)
+        return draw(image_path, out_dir, draw_type='box_2d', object_ids=object_ids, object_types=object_types, line_thickness=line_thickness, colors=colors, quiet=quiet)
 
 
-    def bounding_box_3d(self, image_path, out_dir, object_ids=None, object_types=None, line_thickness=1, colors=None):
+    def bounding_box_3d(self, image_path, out_dir, object_ids=None, object_types=None, line_thickness=1, colors=None, quiet=False):
         """
-        Generates images annotated with 3d bounding boxes for datasets downloaded from the Platform. Optional filter on 
+        Generates images annotated with 3d bounding boxes for datasets downloaded from the Platform. Optional filter on
         object_ids or object_types (must choose a single filter).
-        
+
         Parameters
         ----------
         image_path : str
-            Path to of specific image file to draw the boxes for.  
+            Path to of specific image file to draw the boxes for.
         out_dir : str
             File path to directory where the image should be saved to.
         object_ids : list[int]
@@ -53,22 +60,29 @@ class annotations:
         object_types: list[str]
             Filter for the object types to annotate. If not provided, all object types will get annotated. Choose either id or type filter.
         line_thickness: int
-            Desired line thickness for box outline. 
+            Desired line thickness for box outline.
         colors: dict
             Dictionary of colors to use for each object type where each color is a tuple of 3 integers (R, G, B). For example: colors={'Car': (255, 0, 0)}
+        quiet: bool
+            If True, suppress print output. Useful for CLI/automation.
+
+        Returns
+        -------
+        str or None
+            Path to the saved annotated image, or None if an error occurred.
         """
-        draw(image_path, out_dir, draw_type='box_3d', object_ids=object_ids, object_types=object_types, line_thickness=line_thickness, colors=colors)
+        return draw(image_path, out_dir, draw_type='box_3d', object_ids=object_ids, object_types=object_types, line_thickness=line_thickness, colors=colors, quiet=quiet)
 
 
-    def segmentation(self, image_path, out_dir, object_ids=None, object_types=None, line_thickness=1, colors=None):
+    def segmentation(self, image_path, out_dir, object_ids=None, object_types=None, line_thickness=1, colors=None, quiet=False):
         """
-        Generates images annotated with outlines around objects for datasets downloaded from the Platform. Optional filter on 
+        Generates images annotated with outlines around objects for datasets downloaded from the Platform. Optional filter on
         object_ids or object_types (must choose a single filter).
-        
+
         Parameters
         ----------
         image_path : str
-            Path to of specific image file to draw the boxes for.  
+            Path to of specific image file to draw the boxes for.
         out_dir : str
             File path to directory where the image should be saved to.
         object_ids : list[int]
@@ -79,8 +93,15 @@ class annotations:
             Desired line thickness for object segmentation outline.
         colors: dict
             Dictionary of colors to use for each object type where each color is a tuple of 3 integers (R, G, B). For example: colors={'Car': (255, 0, 0)}
+        quiet: bool
+            If True, suppress print output. Useful for CLI/automation.
+
+        Returns
+        -------
+        str or None
+            Path to the saved annotated image, or None if an error occurred.
         """
-        draw(image_path, out_dir, draw_type='segmentation', object_ids=object_ids, object_types=object_types, line_thickness=line_thickness, colors=colors)
+        return draw(image_path, out_dir, draw_type='segmentation', object_ids=object_ids, object_types=object_types, line_thickness=line_thickness, colors=colors, quiet=quiet)
 
 
     def dump_classification(self, datadir, outdir, mapfile=None):

anatools/annotations/draw.py

@@ -4,14 +4,14 @@ import json
 import os
 
 
-def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=None, line_thickness=1, colors=None): 
+def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=None, line_thickness=1, colors=None, quiet=False):
     """
     This function handles the io and draws the right type of annotation on the image.
 
     Parameters
     ----------
     image_path : str
-        Path to of specific image file to draw the boxes for.  
+        Path to of specific image file to draw the boxes for.
     out_dir : str
         File path to directory where the image should be saved to.
     draw_type : str
@@ -24,15 +24,24 @@ def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=
         Desired line thickness for box outline.
     colors: dict
         Dictionary of colors to use for each object type. Must provide a color for each object type specified in the filter.
+    quiet: bool
+        If True, suppress print output. Useful for CLI/automation.
+
+    Returns
+    -------
+    str or None
+        Path to the saved annotated image, or None if an error occurred.
     """
 
     if not os.path.exists(image_path):
-        print('Incorrect path to images: ' + image_path)
-        return
+        if not quiet:
+            print('Incorrect path to images: ' + image_path)
+        return None
 
     if object_types and object_ids:
-        print('Provide either object_types OR object_ids. ')
-        return
+        if not quiet:
+            print('Provide either object_types OR object_ids. ')
+        return None
 
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
@@ -47,8 +56,8 @@ def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=
     file.close()
     
     annotation_ids = [data['id'] for data in annotations['annotations']]
-    if object_ids is not None and not check_lists(annotation_ids, object_ids, 'object_ids'):
-        return
+    if object_ids is not None and not check_lists(annotation_ids, object_ids, 'object_ids', quiet=quiet):
+        return None
     
     
     metadata_file = root_dir+'/metadata/'+image_name+'-metadata.json'
@@ -62,8 +71,8 @@ def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=
     if object_ids:
         object_data = [data for data in metadata['objects'] if data['id'] in object_ids]
     elif object_types is not None:
-        if not check_lists(metadata_types, object_types, 'object_types'):
-            return  
+        if not check_lists(metadata_types, object_types, 'object_types', quiet=quiet):
+            return None
         object_data = [data for data in metadata['objects'] if data['type'] in object_types]
     else:
         object_data = [data for data in metadata['objects']]
@@ -74,14 +83,15 @@ def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=
             generate_color = [int(val) for val in np.random.randint(0, 255, 3)]
             type_colors[type] = tuple(generate_color)
     else: type_colors = colors
-    
+
 
     draw_img = Image.open(image_path)
     for object in annotations['annotations']:
         if any(object['id'] == d['id'] for d in object_data):
             color_info = [data for data in object_data if object['id'] == data['id']]
             if color_info[0]['type'] not in type_colors:
-                print(f'Color for {color_info[0]["type"]} not found in colors dictionary. Skipping object.')
+                if not quiet:
+                    print(f'Color for {color_info[0]["type"]} not found in colors dictionary. Skipping object.')
                 continue
             if draw_type == 'box_2d':
                 draw_img = box_2d(object['bbox'], draw_img, line_thickness, type_colors[color_info[0]['type']])
@@ -90,11 +100,14 @@ def draw(image_path, out_dir, draw_type='box_2d', object_ids=None, object_types=
             elif draw_type == 'segmentation':
                 draw_img = segmentation(object['segmentation'], draw_img, line_thickness, type_colors[color_info[0]['type']])
             else:
-                print('Provide either box_2d, box_3d, or segmentation')
+                if not quiet:
+                    print('Provide either box_2d, box_3d, or segmentation')
 
     outimg = out_dir+'/'+image_name+'-annotated-'+draw_type+'.'+image_ext
     draw_img.save(outimg)
-    print(f'Image saved to {outimg}')
+    if not quiet:
+        print(f'Image saved to {outimg}')
+    return outimg
 
 
 def box_2d(coordinates, bbox_img, width, outline):
@@ -193,7 +206,7 @@ def segmentation(coordinates, draw_img, width, color):
     return draw_img
 
 
-def check_lists(actual, expected, name_to_check):
+def check_lists(actual, expected, name_to_check, quiet=False):
     """
     Helper function that checks if one list is in another for validation on draw inputs.
 
@@ -205,16 +218,19 @@ def check_lists(actual, expected, name_to_check):
         The expected list that is provided from the user.
     name_to_check: str
         Name of parameter to check (either object_id or object_type).
+    quiet: bool
+        If True, suppress print output.
 
     Returns
     -------
     bool
         True if lists are matching, False otherwise.
     """
-    
+
     if not set(expected).issubset(set(actual)):
         out_of_bounds_check= list(set(expected) - set(actual))
-        print(f'Provided {name_to_check} list has the following out of bounds: {out_of_bounds_check}. Please rerun with valid list. \nHere are all the {name_to_check} that can get annotated: ')
-        print(list(set(actual)))
+        if not quiet:
+            print(f'Provided {name_to_check} list has the following out of bounds: {out_of_bounds_check}. Please rerun with valid list. \nHere are all the {name_to_check} that can get annotated: ')
+            print(list(set(actual)))
         return False
     return True

{anatools-5.1.28.data → anatools-6.0.1.data}/scripts/anadeploy

@@ -332,6 +332,7 @@ try:
                         while resp not in [str(i) for i in range(len(channels)+1)]:
                             resp = input(f'Invalid input, please enter a number between 0 and {len(channels)}: ')
                         remotechannel = channels[int(resp)-1]
+                        print_color(f"Selected channel: {remotechannel['name']}", color='brand')
                         if volumes != remotechannel['volumes']:
                             client.edit_channel(channelId=remotechannel['channelId'], volumes=volumes)
                             remotechannel = client.get_channels(channelId=remotechannel['channelId'])[0]
@@ -346,6 +347,7 @@ try:
             if channels == False or len(channels) == 0: raise Exception(f"Channel {args.channelId} not found")
             remotechannel = channels[0]
         starttime = time.time()
+        client.interactive = True
         deploymentId = client.deploy_channel(channelId=remotechannel['channelId'], channelfile=args.channel)
         print('Registering Channel Image...', flush=True)
         registerstart = time.time()
@@ -493,6 +495,7 @@ try:
                         while resp not in [str(i) for i in range(len(services)+1)]:
                             resp = input(f'Invalid input, please enter a number between 0 and {len(services)}: ')
                         remoteservice = services[int(resp)-1]
+                        print_color(f"Selected service: {remoteservice['name']}", color='brand')
                         if volumes != remoteservice['volumes']:
                             client.edit_service(serviceId=remoteservice['serviceId'], volumes=volumes)
                             remoteservice = client.get_services(serviceId=remoteservice['serviceId'])[0]
@@ -510,6 +513,7 @@ try:
                 client.edit_service(serviceId=remoteservice['serviceId'], volumes=volumes)
                 remoteservice = client.get_services(serviceId=remoteservice['serviceId'])[0]
         starttime = time.time()
+        client.interactive = True
         deploymentId = client.deploy_service(serviceId=remoteservice['serviceId'], servicefile=args.service)
         print('Registering Service Image...', flush=True)
         registerstart = time.time()