np-services 0.1.62__py3-none-any.whl → 0.1.73__py3-none-any.whl

np_services/open_ephys.py

@@ -1,378 +1,377 @@
-import enum
-import json
-import os
-import pathlib
-import shutil
-import socket
-import sys
-import time
-from typing import Any, Optional, Sequence
-
-import np_config
-import np_logging
-import requests
-import npc_ephys
-
-import np_services.utils as utils
-from np_services.protocols import TestError
-
-# global vars -------------------------------------------------------------------------- #
-logger = np_logging.getLogger(__name__)  # logs will show full module path
-
-__name = "OpenEphys"  # Service protocol operations will see just the 'class' name
-
-exc: Optional[BaseException] = None
-initialized: float = 0
-"`time.time()` when the service was initialized."
-
-try:
-    host: str = np_config.Rig().Acq
-except ValueError:
-    logger.warning("Not connected to a rig: `OpenEphys.host` needs to be set manually.")
-port: str | int = 37497  # 1-800-EPHYS
-latest_start: float = 0
-"`time.time()` when the service was last started via `start()`."
-
-# for launching:
-rsc_app_id = "open-ephys"
-
-# device records:
-gb_per_hr: int | float = 250  # per drive
-min_rec_hr: int | float = 2
-pretest_duration_sec: int | float = 0.5
-
-# for resulting data:
-folder: str  #! required
-"The string that will be sent to Open Ephys to name the recording: typically `0123456789_366122_20220618`"
-data_files: list[pathlib.Path] = []
-"Storage for paths collected over the experiment."
-data_root: Optional[pathlib.Path] = None
-
-# for validation
-sync_path: Optional[pathlib.Path] = None
-
-# -------------------------------------------------------------------------------------- #
-
-
-class State(enum.Enum):
-    idle = "IDLE"
-    acquire = "ACQUIRE"
-    record = "RECORD"
-
-
-class Endpoint(enum.Enum):
-    status = "status"
-    recording = "recording"
-    processors = "processors"
-    message = "message"
-
-
-def launch() -> None:
-    utils.start_rsc_app(host, rsc_app_id)
-
-
-def pretest() -> None:
-    logger.info("OpenEphys | Starting pretest")
-    global folder
-    folder = "_pretest_"
-    initialize()
-    test()
-    try:
-        start()
-        time.sleep(pretest_duration_sec)
-        verify()
-    finally:
-        stop()
-    finalize()
-    validate()
-    logger.info("OpenEphys | Pretest passed")
-
-def url(endpoint: Endpoint):
-    return f"http://{host}:{port}/api/{endpoint.value}"
-
-
-def get_state() -> requests.Response:
-    mode = requests.get(u := url(Endpoint.status)).json().get("mode")
-    logger.debug("%s -> get mode: %s", u, mode)
-    return mode
-
-
-def set_state(state: State) -> requests.Response:
-    msg = {"mode": state.value}
-    mode = requests.put(u := url(Endpoint.status), json.dumps(msg))
-    logger.debug("%s <- set mode: %s", u, state.value)
-    return mode
-
-
-def is_connected() -> bool:
-    global exc
-
-    if not utils.is_online(host):
-        exc = TestError(
-            f"OpenEphys | No response from {host}: may be offline or unreachable"
-        )
-        return False
-
-    try:
-        state = get_state()
-    except requests.RequestException:
-        exc = TestError(
-            f"OpenEphys | No response from Open Ephys http server: is the software started?"
-        )
-        return False
-    else:
-        if not any(_.value == state for _ in State):
-            exc = TestError(f"OpenEphys | Unexpected state: {state}")
-            return False
-
-    return True
-
-
-def initialize() -> None:
-    logger.info("OpenEphys | Initializing")
-    global data_files
-    data_files = []
-    sync_path = None
-    global initialized
-    initialized = time.time()
-    global folder
-    set_folder(folder)
-
-
-def get_required_disk_gb() -> int | float:
-    """The minimum amount of free disk space required to start recording."""
-    return gb_per_hr * min_rec_hr
-
-
-def is_disk_space_ok() -> bool:
-    global exc
-    exc = None
-    required = get_required_disk_gb()
-    for data_root in get_data_roots():
-        try:
-            free = utils.free_gb(data_root)
-        except FileNotFoundError as e:
-            exc = e
-            logger.exception(f"{__name} data path not accessible: {data_root}")
-        else:
-            logger.info(
-                "%s free disk space on %s: %s GB", __name, data_root.drive, free
-            )
-            if free < required:
-                exc = ValueError(
-                    f"{__name} free disk space on {data_root.drive} doesn't meet minimum of {required} GB"
-                )
-    if exc:
-        return False
-    return True
-
-
-def test() -> None:
-    logger.info("OpenEphys | Testing")
-    if not is_connected():
-        if exc:
-            raise TestError(f"Acq computer {host} isn't responding, or OpenEphys isn't open") from exc
-    gb = get_required_disk_gb()
-    if not is_disk_space_ok():
-        raise TestError(
-            f"{__name} free disk space on one or more recording drives doesn't meet minimum of {gb} GB"
-        ) from exc
-    unlock_previous_recording()
-
-
-def is_started() -> bool:
-    if get_state() == State.record.value:
-        return True
-    return False
-
-
-def is_ready_to_start() -> bool:
-    if get_state() == State.acquire.value:
-        return True
-    return False
-
-
-def start() -> None:
-    logger.info("OpenEphys | Starting recording")
-    if is_started():
-        logger.warning("OpenEphys is already started")
-        return
-    if not is_ready_to_start():
-        set_state(State.acquire)
-        time.sleep(0.5)
-    global latest_start
-    latest_start = time.time()
-    set_state(State.record)
-
-
-def stop() -> None:
-    logger.info("OpenEphys | Stopping recording")
-    set_state(State.acquire)
-
-
-def finalize() -> None:
-    logger.info("OpenEphys | Finalizing")
-    data_files.extend(get_latest_data_dirs())
-    unlock_previous_recording()
-
-
-def set_folder(
-    name: str, prepend_text: str = "", append_text: str = ""
-) -> None:
-    """Recording folder string"""
-    recording = requests.get(url(Endpoint.recording)).json()
-
-    if name == "":
-        name = "_"
-        logger.warning(
-            "OpenEphys | Recording directory cannot be empty, replaced with underscore: %s",
-            name,
-        )
-    if "." in name:
-        name.replace(".", "_")
-        logger.warning(
-            "OpenEphys | Recording directory cannot contain periods, replaced with underscores: %s",
-            name,
-        )
-
-    recording["base_text"] = name
-    recording["prepend_text"] = prepend_text
-    recording["append_text"] = append_text
-    logger.debug(
-        "OpenEphys | Setting recording directory to: %s",
-        prepend_text + name + append_text,
-    )
-    response = requests.put(url(Endpoint.recording), json.dumps(recording))
-    time.sleep(0.1)
-    if (actual := response.json().get("base_text")) != name:
-        raise TestError(
-            f"OpenEphys | Set folder to {name}, but software shows: {actual}"
-        )
-
-
-def get_folder() -> str | None:
-    return requests.get(url(Endpoint.recording)).json().get("base_text")
-
-
-def clear_open_ephys_name() -> None:
-    set_folder("_temp_")
-
-
-def set_idle():
-    "Should be called before sending any configuration to Open Ephys"
-    if is_started():
-        stop()
-    time.sleep(0.5)
-    set_state(State.idle)
-
-
-def unlock_previous_recording():
-    "stop rec/acquiring | set name to _temp_ | record briefly | acquire | set name to folder"
-    logger.debug("OpenEphys | Unlocking previous recording")
-    set_idle()
-    time.sleep(0.5)
-    clear_open_ephys_name()
-    time.sleep(0.5)
-    start()
-    time.sleep(0.5)
-    stop()
-    time.sleep(0.5)
-    global folder
-    set_folder(folder)
-
-
-def get_record_nodes() -> list[dict[str, Any]]:
-    """Returns a list of record node info dicts, incl keys `node_id`, `parent_directory`"""
-    return requests.get(url(Endpoint.recording)).json().get("record_nodes", None) or []
-
-
-def get_data_roots() -> list[pathlib.Path]:
-    return [
-        pathlib.Path(f"//{host}/{_['parent_directory'].replace(':','')}")
-        for _ in get_record_nodes()
-    ]
-
-
-def get_latest_data_dirs() -> list[pathlib.Path]:
-    """Returns the path to the latest data folder, based on the latest modified time"""
-    dirs = []
-    for root in get_data_roots():
-        if subfolders := [
-            sub
-            for sub in root.iterdir()
-            if sub.is_dir()
-            and not any(
-                _ in str(sub) for _ in ["System Volume Information", "$RECYCLE.BIN"]
-            )
-        ]:
-            subfolders.sort(key=lambda _: _.stat().st_ctime)
-            dirs.append(subfolders[-1])
-    return dirs
-
-def check_files_increasing_in_size() -> None:
-    for data_dir in get_latest_data_dirs():
-        for file in reversed(
-            utils.get_files_created_between(
-                data_dir, "*/*/*/continuous/*/sample_numbers.npy", latest_start
-            )
-        ):
-            if utils.is_file_growing(file):
-                break
-        else:
-            raise TestError(
-                f"OpenEphys | Data file(s) not increasing in size in {data_dir}"
-            )
-
-def verify() -> None:
-    logger.debug("OpenEphys | Verifying")
-    check_files_increasing_in_size()    
-    logger.info(
-        "OpenEphys | Verified files are increasing in size for all Record Nodes"
-    )
-
-
-def validate() -> None:
-    logger.info(f"OpenEphys | Validating")
-    npc_ephys.validate_ephys(
-        root_paths=data_files,
-        sync_path_or_dataset=sync_path,
-        ignore_small_folders=True,
-    )
-    logger.info(f"OpenEphys | Validated data {'with' if sync_path else 'without'} sync")
-
-def set_ref(ext_tip="TIP"):
-    # for port in [0, 1, 2]:
-    #     for slot in [0, 1, 2]:
-
-    slot = 2  #! Test
-    port = 1  #! Test
-    dock = 1  # TODO may be 1 or 2 with firmware upgrade
-    tip_ref_msg = {"text": f"NP REFERENCE {slot} {port} {dock} {ext_tip}"}
-    # logger.info(f"sending ...
-    # return
-    requests.put(
-        "http://localhost:37497/api/processors/100/config", json.dumps(tip_ref_msg)
-    )
-    time.sleep(3)
-
-
-# TODO set up everything possible from here to avoid accidentally changed settings ?
-# probe channels
-# sampling rate
-# tip ref
-# signal chain?
-# acq drive letters
-
-"""
-if __name__ == "__main__":
-    r = requests.get(Endpoint.recording)
-    print((r.json()['current_directory_name'], r.json()['prepend_text'], r.json()['append_text']))
-        
-    r = EphysHTTP.set_folder(path = "mouseID_", prepend_text="sessionID", append_text="_date")
-    print((r.json()['current_directory_name'], r.json()['prepend_text'], r.json()['append_text']))
-    
-    r = EphysHTTP.set_folder(path = "mouse", prepend_text="session", append_text="date")
-    print((r.json()['current_directory_name'], r.json()['prepend_text'], r.json()['append_text']))
-    
-    print((r.json()['base_text'])) # fails as of 06/23 https://github.com/open-ephys/plugin-GUI/pull/514
-"""
+import enum
+import json
+import os
+import pathlib
+import shutil
+import socket
+import sys
+import time
+from typing import Any, Optional, Sequence
+
+import np_config
+import np_logging
+import requests
+
+import np_services.utils as utils
+from np_services.protocols import TestError
+
+# global vars -------------------------------------------------------------------------- #
+logger = np_logging.getLogger(__name__)  # logs will show full module path
+
+__name = "OpenEphys"  # Service protocol operations will see just the 'class' name
+
+exc: Optional[BaseException] = None
+initialized: float = 0
+"`time.time()` when the service was initialized."
+
+try:
+    host: str = np_config.Rig().Acq
+except ValueError:
+    logger.warning("Not connected to a rig: `OpenEphys.host` needs to be set manually.")
+port: str | int = 37497  # 1-800-EPHYS
+latest_start: float = 0
+"`time.time()` when the service was last started via `start()`."
+
+# for launching:
+rsc_app_id = "open-ephys"
+
+# device records:
+gb_per_hr: int | float = 250  # per drive
+min_rec_hr: int | float = 2
+pretest_duration_sec: int | float = 0.5
+
+# for resulting data:
+folder: str  #! required
+"The string that will be sent to Open Ephys to name the recording: typically `0123456789_366122_20220618`"
+data_files: list[pathlib.Path] = []
+"Storage for paths collected over the experiment."
+data_root: Optional[pathlib.Path] = None
+
+# for validation
+sync_path: Optional[pathlib.Path] = None
+
+# -------------------------------------------------------------------------------------- #
+
+
+class State(enum.Enum):
+    idle = "IDLE"
+    acquire = "ACQUIRE"
+    record = "RECORD"
+
+
+class Endpoint(enum.Enum):
+    status = "status"
+    recording = "recording"
+    processors = "processors"
+    message = "message"
+
+
+def launch() -> None:
+    utils.start_rsc_app(host, rsc_app_id)
+
+
+def pretest() -> None:
+    logger.info("OpenEphys | Starting pretest")
+    global folder
+    folder = "_pretest_"
+    initialize()
+    test()
+    try:
+        start()
+        time.sleep(pretest_duration_sec)
+        verify()
+    finally:
+        stop()
+    finalize()
+    validate()
+    logger.info("OpenEphys | Pretest passed")
+
+def url(endpoint: Endpoint):
+    return f"http://{host}:{port}/api/{endpoint.value}"
+
+
+def get_state() -> requests.Response:
+    mode = requests.get(u := url(Endpoint.status)).json().get("mode")
+    logger.debug("%s -> get mode: %s", u, mode)
+    return mode
+
+
+def set_state(state: State) -> requests.Response:
+    msg = {"mode": state.value}
+    mode = requests.put(u := url(Endpoint.status), json.dumps(msg))
+    logger.debug("%s <- set mode: %s", u, state.value)
+    return mode
+
+
+def is_connected() -> bool:
+    global exc
+
+    if not utils.is_online(host):
+        exc = TestError(
+            f"OpenEphys | No response from {host}: may be offline or unreachable"
+        )
+        return False
+
+    try:
+        state = get_state()
+    except requests.RequestException:
+        exc = TestError(
+            f"OpenEphys | No response from Open Ephys http server: is the software started?"
+        )
+        return False
+    else:
+        if not any(_.value == state for _ in State):
+            exc = TestError(f"OpenEphys | Unexpected state: {state}")
+            return False
+
+    return True
+
+
+def initialize() -> None:
+    logger.info("OpenEphys | Initializing")
+    global data_files
+    data_files = []
+    global initialized
+    initialized = time.time()
+    global folder
+    set_folder(folder)
+
+
+def get_required_disk_gb() -> int | float:
+    """The minimum amount of free disk space required to start recording."""
+    return gb_per_hr * min_rec_hr
+
+
+def is_disk_space_ok() -> bool:
+    global exc
+    exc = None
+    required = get_required_disk_gb()
+    for data_root in get_data_roots():
+        try:
+            free = utils.free_gb(data_root)
+        except FileNotFoundError as e:
+            exc = e
+            logger.exception(f"{__name} data path not accessible: {data_root}")
+        else:
+            logger.info(
+                "%s free disk space on %s: %s GB", __name, data_root.drive, free
+            )
+            if free < required:
+                exc = ValueError(
+                    f"{__name} free disk space on {data_root.drive} doesn't meet minimum of {required} GB"
+                )
+    if exc:
+        return False
+    return True
+
+
+def test() -> None:
+    logger.info("OpenEphys | Testing")
+    if not is_connected():
+        if exc:
+            raise TestError(f"Acq computer {host} isn't responding, or OpenEphys isn't open") from exc
+    gb = get_required_disk_gb()
+    if not is_disk_space_ok():
+        raise TestError(
+            f"{__name} free disk space on one or more recording drives doesn't meet minimum of {gb} GB"
+        ) from exc
+    unlock_previous_recording()
+
+
+def is_started() -> bool:
+    if get_state() == State.record.value:
+        return True
+    return False
+
+
+def is_ready_to_start() -> bool:
+    if get_state() == State.acquire.value:
+        return True
+    return False
+
+
+def start() -> None:
+    logger.info("OpenEphys | Starting recording")
+    if is_started():
+        logger.warning("OpenEphys is already started")
+        return
+    if not is_ready_to_start():
+        set_state(State.acquire)
+        time.sleep(0.5)
+    global latest_start
+    latest_start = time.time()
+    set_state(State.record)
+
+
+def stop() -> None:
+    logger.info("OpenEphys | Stopping recording")
+    set_state(State.acquire)
+
+
+def finalize() -> None:
+    logger.info("OpenEphys | Finalizing")
+    data_files.extend(get_latest_data_dirs())
+    unlock_previous_recording()
+
+
+def set_folder(
+    name: str, prepend_text: str = "", append_text: str = ""
+) -> None:
+    """Recording folder string"""
+    recording = requests.get(url(Endpoint.recording)).json()
+
+    if name == "":
+        name = "_"
+        logger.warning(
+            "OpenEphys | Recording directory cannot be empty, replaced with underscore: %s",
+            name,
+        )
+    if "." in name:
+        name.replace(".", "_")
+        logger.warning(
+            "OpenEphys | Recording directory cannot contain periods, replaced with underscores: %s",
+            name,
+        )
+
+    recording["base_text"] = name
+    recording["prepend_text"] = prepend_text
+    recording["append_text"] = append_text
+    logger.debug(
+        "OpenEphys | Setting recording directory to: %s",
+        prepend_text + name + append_text,
+    )
+    response = requests.put(url(Endpoint.recording), json.dumps(recording))
+    time.sleep(0.1)
+    if (actual := response.json().get("base_text")) != name:
+        raise TestError(
+            f"OpenEphys | Set folder to {name}, but software shows: {actual}"
+        )
+
+
+def get_folder() -> str | None:
+    return requests.get(url(Endpoint.recording)).json().get("base_text")
+
+
+def clear_open_ephys_name() -> None:
+    set_folder("_temp_")
+
+
+def set_idle():
+    "Should be called before sending any configuration to Open Ephys"
+    if is_started():
+        stop()
+    time.sleep(0.5)
+    set_state(State.idle)
+
+
+def unlock_previous_recording():
+    "stop rec/acquiring | set name to _temp_ | record briefly | acquire | set name to folder"
+    logger.debug("OpenEphys | Unlocking previous recording")
+    set_idle()
+    time.sleep(0.5)
+    clear_open_ephys_name()
+    time.sleep(0.5)
+    start()
+    time.sleep(0.5)
+    stop()
+    time.sleep(0.5)
+    global folder
+    set_folder(folder)
+
+
+def get_record_nodes() -> list[dict[str, Any]]:
+    """Returns a list of record node info dicts, incl keys `node_id`, `parent_directory`"""
+    return requests.get(url(Endpoint.recording)).json().get("record_nodes", None) or []
+
+
+def get_data_roots() -> list[pathlib.Path]:
+    return [
+        pathlib.Path(f"//{host}/{_['parent_directory'].replace(':','')}")
+        for _ in get_record_nodes()
+    ]
+
+
+def get_latest_data_dirs() -> list[pathlib.Path]:
+    """Returns the path to the latest data folder, based on the latest modified time"""
+    dirs = []
+    for root in get_data_roots():
+        if subfolders := [
+            sub
+            for sub in root.iterdir()
+            if sub.is_dir()
+            and not any(
+                _ in str(sub) for _ in ["System Volume Information", "$RECYCLE.BIN"]
+            )
+        ]:
+            subfolders.sort(key=lambda _: _.stat().st_ctime)
+            dirs.append(subfolders[-1])
+    return dirs
+
+def check_files_increasing_in_size() -> None:
+    for data_dir in get_latest_data_dirs():
+        for file in reversed(
+            utils.get_files_created_between(
+                data_dir, "*/*/*/continuous/*/sample_numbers.npy", latest_start
+            )
+        ):
+            if utils.is_file_growing(file):
+                break
+        else:
+            raise TestError(
+                f"OpenEphys | Data file(s) not increasing in size in {data_dir}"
+            )
+
+def verify() -> None:
+    logger.debug("OpenEphys | Verifying")
+    check_files_increasing_in_size()    
+    logger.info(
+        "OpenEphys | Verified files are increasing in size for all Record Nodes"
+    )
+
+
+def validate() -> None:
+    logger.info(f"OpenEphys | Validating")
+    import npc_ephys
+    npc_ephys.validate_ephys(
+        root_paths=data_files,
+        sync_path_or_dataset=sync_path,
+        ignore_small_folders=True,
+    )
+    logger.info(f"OpenEphys | Validated data {'with' if sync_path else 'without'} sync")
+
+def set_ref(ext_tip="TIP"):
+    # for port in [0, 1, 2]:
+    #     for slot in [0, 1, 2]:
+
+    slot = 2  #! Test
+    port = 1  #! Test
+    dock = 1  # TODO may be 1 or 2 with firmware upgrade
+    tip_ref_msg = {"text": f"NP REFERENCE {slot} {port} {dock} {ext_tip}"}
+    # logger.info(f"sending ...
+    # return
+    requests.put(
+        "http://localhost:37497/api/processors/100/config", json.dumps(tip_ref_msg)
+    )
+    time.sleep(3)
+
+
+# TODO set up everything possible from here to avoid accidentally changed settings ?
+# probe channels
+# sampling rate
+# tip ref
+# signal chain?
+# acq drive letters
+
+"""
+if __name__ == "__main__":
+    r = requests.get(Endpoint.recording)
+    print((r.json()['current_directory_name'], r.json()['prepend_text'], r.json()['append_text']))
+        
+    r = EphysHTTP.set_folder(path = "mouseID_", prepend_text="sessionID", append_text="_date")
+    print((r.json()['current_directory_name'], r.json()['prepend_text'], r.json()['append_text']))
+    
+    r = EphysHTTP.set_folder(path = "mouse", prepend_text="session", append_text="date")
+    print((r.json()['current_directory_name'], r.json()['prepend_text'], r.json()['append_text']))
+    
+    print((r.json()['base_text'])) # fails as of 06/23 https://github.com/open-ephys/plugin-GUI/pull/514
+"""