dsa-helpers 1.0.4.dev1__tar.gz → 1.0.5.dev0__tar.gz

{dsa_helpers-1.0.4.dev1/dsa_helpers.egg-info → dsa_helpers-1.0.5.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.0.4.dev1
+Version: 1.0.5.dev0
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

dsa_helpers-1.0.5.dev0/dsa_helpers/cli_utils.py

@@ -0,0 +1,183 @@
+from collections import deque
+import psutil, threading, time
+import numpy as np
+
+
+class SystemMonitor:
+    def __init__(self, interval=0.5):
+        self.interval = interval
+        self.cpu_percentages = deque(maxlen=100)
+        self.memory_usage = deque(maxlen=100)
+        self.io_wait = deque(maxlen=100)
+        self.cpu_per_core = deque(maxlen=100)  # Track per-core usage
+        self.memory_bandwidth = deque(maxlen=100)
+        self.io_stats = deque(maxlen=100)
+        self.stop_flag = False
+        self.process = psutil.Process()
+
+    def start(self):
+        self.stop_flag = False
+        self.monitor_thread = threading.Thread(target=self._monitor)
+        self.monitor_thread.start()
+
+    def stop(self):
+        self.stop_flag = True
+        self.monitor_thread.join()
+
+        # Calculate statistics with safety checks
+        cpu_stats = {
+            "mean": (
+                np.mean(self.cpu_percentages)
+                if len(self.cpu_percentages) > 0
+                else 0
+            ),
+            "max": (
+                np.max(self.cpu_percentages)
+                if len(self.cpu_percentages) > 0
+                else 0
+            ),
+            "min": (
+                np.min(self.cpu_percentages)
+                if len(self.cpu_percentages) > 0
+                else 0
+            ),
+            "per_core_mean": (
+                np.mean(self.cpu_per_core, axis=0)
+                if len(self.cpu_per_core) > 0
+                else np.zeros(psutil.cpu_count())
+            ),
+            "per_core_max": (
+                np.max(self.cpu_per_core, axis=0)
+                if len(self.cpu_per_core) > 0
+                else np.zeros(psutil.cpu_count())
+            ),
+            "active_cores_mean": (
+                np.mean(
+                    [
+                        sum(1 for x in cores if x > 10)
+                        for cores in self.cpu_per_core
+                    ]
+                )
+                if len(self.cpu_per_core) > 0
+                else 0
+            ),
+        }
+
+        mem_stats = {
+            "mean": (
+                np.mean(self.memory_usage) if len(self.memory_usage) > 0 else 0
+            ),
+            "max": (
+                np.max(self.memory_usage) if len(self.memory_usage) > 0 else 0
+            ),
+            "min": (
+                np.min(self.memory_usage) if len(self.memory_usage) > 0 else 0
+            ),
+        }
+
+        io_stats = {
+            "wait_mean": np.mean(self.io_wait) if len(self.io_wait) > 0 else 0,
+            "wait_max": np.max(self.io_wait) if len(self.io_wait) > 0 else 0,
+            "throughput_read": (
+                np.mean(
+                    [
+                        sum(disk["read_bytes"] for disk in x["disk"].values())
+                        / x["time_delta"]
+                        for x in self.io_stats
+                    ]
+                )
+                / 1024
+                / 1024
+                if len(self.io_stats) > 0
+                else 0
+            ),
+            "throughput_write": (
+                np.mean(
+                    [
+                        sum(disk["write_bytes"] for disk in x["disk"].values())
+                        / x["time_delta"]
+                        for x in self.io_stats
+                    ]
+                )
+                / 1024
+                / 1024
+                if len(self.io_stats) > 0
+                else 0
+            ),
+            "network_read": (
+                np.mean(
+                    [
+                        x["network"]["bytes_recv"] / x["time_delta"]
+                        for x in self.io_stats
+                    ]
+                )
+                / 1024
+                / 1024
+                if len(self.io_stats) > 0
+                else 0
+            ),
+            "network_write": (
+                np.mean(
+                    [
+                        x["network"]["bytes_sent"] / x["time_delta"]
+                        for x in self.io_stats
+                    ]
+                )
+                / 1024
+                / 1024
+                if len(self.io_stats) > 0
+                else 0
+            ),
+        }
+
+        return {"cpu": cpu_stats, "memory": mem_stats, "io": io_stats}
+
+    def _monitor(self):
+        last_io = psutil.disk_io_counters(perdisk=True)  # Monitor per-disk
+        last_net = psutil.net_io_counters()  # Add network monitoring
+        last_time = time.time()
+
+        while not self.stop_flag:
+            # CPU usage (overall and per-core)
+            per_core = psutil.cpu_percent(percpu=True)
+            self.cpu_percentages.append(np.mean(per_core))
+            self.cpu_per_core.append(per_core)
+
+            # Memory usage
+            mem = self.process.memory_info()
+            self.memory_usage.append(mem.rss / 1024 / 1024)  # Convert to MB
+
+            # IO wait and throughput
+            cpu_times = psutil.cpu_times_percent()
+            self.io_wait.append(cpu_times.iowait)
+
+            # Enhanced IO monitoring
+            current_io = psutil.disk_io_counters(perdisk=True)
+            current_net = psutil.net_io_counters()
+            current_time = time.time()
+
+            # Calculate both disk and network throughput
+            delta_time = current_time - last_time
+            io_delta = {
+                "disk": {
+                    disk: {
+                        "read_bytes": current_io[disk].read_bytes
+                        - last_io[disk].read_bytes,
+                        "write_bytes": current_io[disk].write_bytes
+                        - last_io[disk].write_bytes,
+                    }
+                    for disk in current_io
+                },
+                "network": {
+                    "bytes_recv": current_net.bytes_recv - last_net.bytes_recv,
+                    "bytes_sent": current_net.bytes_sent - last_net.bytes_sent,
+                },
+                "time_delta": delta_time,
+            }
+            self.io_stats.append(io_delta)
+
+            last_io = current_io
+            last_net = current_net
+            last_time = current_time
+
+            time.sleep(self.interval)

{dsa_helpers-1.0.4.dev1 → dsa_helpers-1.0.5.dev0}/dsa_helpers/image_utils.py

@@ -89,13 +89,14 @@ def label_mask_to_polygons(
 
         # Convert to shapely polygon objects.
         for data in polygons_dict.values():
-            polygon = Polygon(data["polygon"], holes=data["holes"])
+            if "polygon" in data:
+                polygon = Polygon(data["polygon"], holes=data["holes"])
 
-            # Shift the polygon by the offset.
-            polygon = translate(polygon, xoff=x_offset, yoff=y_offset)
+                # Shift the polygon by the offset.
+                polygon = translate(polygon, xoff=x_offset, yoff=y_offset)
 
-            # Include the polygon if it's greater than the minimum area.
-            if polygon.area >= min_area:
-                polygons.append([polygon, int(label)])
+                # Include the polygon if it's greater than the minimum area.
+                if polygon.area >= min_area:
+                    polygons.append([polygon, int(label)])
 
     return polygons

{dsa_helpers-1.0.4.dev1 → dsa_helpers-1.0.5.dev0/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.0.4.dev1
+Version: 1.0.5.dev0
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-1.0.4.dev1 → dsa_helpers-1.0.5.dev0}/dsa_helpers.egg-info/SOURCES.txt

@@ -8,6 +8,7 @@ docs/requirements.txt
 docs/source/conf.py
 docs/source/index.rst
 dsa_helpers/__init__.py
+dsa_helpers/cli_utils.py
 dsa_helpers/girder_utils.py
 dsa_helpers/image_utils.py
 dsa_helpers/imread.py

{dsa_helpers-1.0.4.dev1 → dsa_helpers-1.0.5.dev0}/pyproject.toml

@@ -35,7 +35,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.0.4.dev1"
+version = "v1.0.5.dev0"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"